This is an older but not too old topic that I thought I would fill in anything that may have been overlooked. I'm thinking practicality of naval vessel design as we expand into space. (It should be noted any civilization with the technology and energy to easily navigate space would not have the same motivations for war that we have today).
Once you can technologically live in space, things like territory, resources, etc. are no longer an issue. The Sun alone provides enough energy to have a huge fusion swarm with quadrillions of people living more comfortably than even the richest of people today can live. I can assume this because here, we are already assuming vast space armadas are able to be built, which would require the same technological levels. So almost anything you would fight over is something that would be far less worth the hassle and threat to swarms of living habitats surrounding the Sun - remember if something were destroyed in space such as a ship, then all that debris becomes unintentional weapons fired in random directions, something the neighborhood is not going to be very appreciative of happening when the fight is over something trivial.
Again, once in space, any kind of resource you could want is much easier to obtain, unless it's a very abstract desire. A single small asteroid or comet is far more valuable than all of Earth's resources because it's much more abundant because it's concentrated which also makes it much easier to get. There would be little gravity well to escape as well. And there's plenty of these objects that it would take a ridiculously long time to run out of them.
But say everything around a star was consumed. If you could do that, than you'd have the technology to do star lifting (gathering resources directly from your star). While to us that's a hard thing to do but technologically possible even today, a civilization we are describing would have no problems doing it. Google star lifting if you want to learn more.
So when discussing such a topic, you already have to make assumptions which you will base your next predictions and reasoning (logic) off. In this case, a space navy capability already assumes a lot about technologies humanity will have gained or mastered in the future.
And there will not be a logical reason to conduct warfare since everything wars are fought over today are generally logical and cold with a trumped up reason (i.e. "I want your gold so I'll tell my people that your people are some sort of threat to my people's existence". Or something like that. The logic is really about getting at some resource). Of course, we would hope at that stage in civilization, we will have become a more secular society and one that has a very sound grasp of the human mind so we will have generally solved many issues that cause abnormal and hurtful behavior such as depression, suicide, homicide, etc., even in cases where it's purely biological since again we should not have any problems providing for people in terms of very high living standards.
We will also assume FTL is either impossible or not yet achievable for some unknown reason. Even without FTL technology and with today's technology, humanity could spread across the entire galaxy in only a couple dozen million years. Which isn't very long at all for cosmic timescales. We could even practically spread out to other galaxies if there became a compelling reason to do so. That would take more time to do, but even if speaking in terms of billions of years, that's still small over cosmic timelines.
With FTL in the picture it just makes any reason to go to war all the more irrational and unlikely (bug again this is where things become more unpredictable). What biological relics will we retain that served an evolutionary purpose at one point in time but would only serve as an illogical motivation in the future. It's worth noting also that human species will start to be more meaningless of a term as any population will evolve (through technology or just biology) as time passes and different environments are settled. So there are a lot of things that could happen which even using my reasoning for having windows will no longer make sense.
Okay, with that out of the way, the reason for windows or a bridge that stands out boils down to easy rationale: Psychology plus practicality.
In the context of modern warfare, even today in naval warfare, windows are not necessary. They have no military value even if your "sensors" (whatever they may be) go out. Ship-to-ship combat has not been fought face-to-face by capital ships for over a century. And in most modern warfare, even a destroyer has been made into the equivalent of a battleship since offensive weaponry simply outpaced armor decades ago. And ever since the ability to launch planes to attach ships was a reality, the effective "gun" range of an aircraft carrier is as far as a plane can fly. Where any gun has maybe 60 miles in extreme context. Say 18" battleship guns with rocket assisted projectiles (which in modern field artillery only gets maximum ranges of about 20-30 km depending on sizes).
I should mention I was a fire officer for a battalion. So me and my 5-man crew served as the brains of any indirect fire support requests. So besides my degrees in math MS and physics BS, I have practical experience in training and applications. So two things emerge from that. The practicality of having large vessels tends to decrease with time, as they simply become large targets, and appear stationary to weapons and vehicles that move at velocities faster than sound.
While I cannot say with certainty what a space navy would look like, I would say it probably wouldn't look very recognizable to any comparable water based navy except for submarines. The barring factor being what size is a practical war vessel. It's simply too difficult to foresee what technologies will lead naval ship sides to evolve into. Small ships are more maneuverable and by any foreseeable technology will be the largest factor in survival, especially when talking about defending against object in space where velocities alone can turn bullets into weapons with the energies of nuclear weaponry (simply from kinetic energy though).
So this is the practical part of the problem. If your ships are not particularly large to begin with, or the size has no bearing on how protected you are should you actually be hit with a futuristic weapon, then it doesn't matter where your bridge is. In fact, the concept of a bridge may become antiquated. And everything will be spread out as much as possible so the ship remains as functional as possible if any one section of it is hit (assuming that being hit is even survivable, which would make large unmaneuvarable ships unlikely as it's a larger investment and risk without any payoff).
Something I can't account for is whether countermeasures in the future to shoot down projectiles being fired at you or shielding against energy-based weapons makes sense to have on larger or smaller craft. There are some conceivable energy weapons which no amount of shielding would protect you from and would radiate the crew of the vessel to death but leave the ship intact. It's worth looking at why a sci-fi novel or movie is trying to do. They very often try to be symbolic and relatable to us. So things are written even knowing the plot is flawed scientifically.
Give an alien invasion of Earth for instance. It would not be a contest if they decided they wanted to kill us. They would send down meteors, viruses, nerve gas, etc and we would die off quickly and helplessly to the point of extinction if they wished it. But that would not make for a good story. So the author often needs to take great liberties in giving humanity a way to win. Such as aliens traveling between stars but not having antivirus software like in Independence Day. Since aliens are meant to usually represent a deep fear of the dark, unknown monsters seared into our brain through evolution, not a true scientifically accurate description of how a war with a hyper advanced space civilization would play out. We haven't even put 1000 people in space total yet. We realistically would have the same chance to win against them as a crippled Bambi would have against a healthy Godzilla.
Next comes psychological reasons, which would be more likely to occur. But I'm basing it off of today's psychology which could drastically change. Future humanity will likely augment brainpower in some fashion. Even if some people object to it there will always be those willing to do it. Those people will likely be the ones to survive more in the future. Between that and more people becoming less afraid of such changes as time goes on, we are unlikely to fathom what future psychology will be like. I will also point out that the reasons apply for any intelligence that I gave in the first paragraph. Whether silicone or carbon based brains should not matter.
But sticking with what we absolutely know, a window serves a vital purpose. Purely psychological ones. It's why people are heavily screened for signs of mental illness before being able to serve on a submarine. We generally don't do well in closed spaces where we also can't see the Sun ever. So windows serve simply as a way for people to stay connected to the outside world psychologically. Just being able to see or be outside on a ship makes someone feel much more connected to the world. And someone in a submarine may get the same freedom to communicate, but would still feel more isolated and cutoff from society.
Humanity is much more of a social animal than some people realize. But most people seem to perceive this at least on some level. And the aesthetic environment can drastically alter the mental health of the personnel on a ship. It's easy for an engineer to design a ship to be as efficient and indestructible as possible. But engineers have historically never been in step with reality when it comes to warfare. Especially if they know nothing about it and, combined with a lack of understanding human psychology, end up designing terrible weapons that never get off the paper.
A good example of this could be a simple one I once encountered at Picatinny Arsenal in New Jersey. They had designed a superior mortar system - on paper. The only problem is the system was supposed to be portable and contained a baseplate that would have realistically required robotic assistance to carry. Again, engineers are not good at designing things practical for people. They are great at making weapons that are perfect for robotic weaponry, but not for a person who is physically and psychologically under stress enough just being in war.
So you could argue all you want about how unnecessary that raised bridge is (which it is today - even on a ship there's no need for a raised over exposed bridge with windows), but even to the commanders it had a psychological effect on when making decisions. Note: even in navigating ports, visual sight is not technically necessary anymore. The bridge being exposed but over-towering is also psychological. It gives the crew somewhere to look to symbolically to gain courage. Or something to at least instill discipline and remind people there is command and control aboard a ship, so it's not without rules or regulations no matter how big or small.
In large cases, it may also serve to intimidate an enemy (or potential enemy/ally) as a projection of the actual power you control. Again, this takes a lot of liberties, since there's a large difference between a naval ship in water and one in space. I am not overly familiar with space psychology but I do know even with windows on shuttles and the space station that people are rigorously tested for any psychological signs of being incompatible with the challenges of space. Even then, a lot of astronauts still have trouble coping with space. I can only imagine that will become harder to manage the further away from Earth people travel. There will only be a feeling of further isolation as distances in space grow and communication isn't even instantaneous anymore from the FTL issues.
Originally, the crews that landed or orbited the moon could not even communicate with Earth on the far side before satellites were so prevalent. Some did pick up odd radio signals from the direction of Saturn. Nothing to suggest aliens or anything unnatural but when isolated, in deep, dark, and cold space, it doesn't take much to make a crew become more anxious, paranoid, etc. A space armada would likely be spaced out to a point where visual contact with friendly or enemy craft will not occur. Just as is often the case in modern naval warfare. So again, I can only use today's psychology and personal experience in war to go on. I tend to think these issues will become easier to deal with given more time and technology, but I have to speculate based on what I do know. Which is only today's psychology.
On a side note: you should be aware that all things in space give off something called black body radiation. So no matter what tricks you may try to pull off, it's virtually impossible to have a truly stealthy space craft. You'll never get it cold enough to look like the background radiation or even close enough to miss at least a suspicious notice. We have crazily accurate abilities to map the background radiation to a thousandth or even more of a kelvin/Celsius. So getting just your body to blend in with this background would take impractical amounts of effort. The effort would actually most likely only draw more attention to your craft since it would be something very anomalous to any civilization. Much more than a natural phenomenon or spacecraft not trying to hide would appear. Which would only most likely make you more likely to be found and make an opponent more likely to judge you to be hostile or have some nefarious business if you don't want to be seen approaching.