Besides the obvious steel entry doors, I am most concerned about air-inlets and exhausts. Electricity for essential things like lighting, ventilation or pumping water is generated by diesel generators. These must have an exhaust somewhere. Wouldn't it be obvious for the enemies to find the spot where exhaust fumes come out of the ground? What's to keep them from pouring some cement down that hole? While we are on in, if this is in a sparsely populated area, would it be sensible to instruct enemy soldiers to shove some dirt into any unknown pipe sticking out from the ground, blocking potential intakes?
Hide from what, exactly?
In and beyond the WWII timeframe, there were different kinds of hidden bunkers.
- Hide from long-range reconnaissance and attack.
The idea with these bunkers is to stay hidden from enemy (photo) recon aircraft and bombs. In WWII, examples include B8 Bergkristall, an underground factory dug by concentration camp prisoners to build jet aircraft. After WWII, with a completely different purpose, think of the bunker under the Greenbrier hotel. These are not supposed to survive with enemy troops camped on top, instead the idea was to defeat the sensors and weapons of the time.
- Camouflaged fighting positions.
Some smaller installations were supposed to remain secure from attack by nearby enemy forces. Being camouflaged into the landscape helped, but often the site was also supposed to fight. Hiding completely would defeat the purpose. An example would be the Maginot fortifications in France or the Swiss reduit. Again, the bunkers were not supposed to remain hidden with enemies directly on top, but here the camouflage was supposed to complicate attack by nearby troops.
- Hide from close search
That's what you are looking for, right? These were quite unusual. I can think of two interesting British examples. One is the bunker for Operation Tracer, the plan to hide a few observers on Gibraltar if the Germans or the Spanish ever took "the Rock." The other are the bunkers of the Auxiliary Units, constructed in the UK in case the Germans invaded. Neither one had to be used in action.
As you can see, the larger the installation, the less likely it was to remain hidden with enemies directly on top. The smaller ones would rely on being quiet, and having their air pipes, exhausts, etc. in places where the enemy would not search.
The Art of Concealment:
Are you trying to hide one from random guys, or people seeking out bunkers? A lot of effort went into this kind of physical secrecy in WWII, more than I can even reasonably discuss. You'll need to do some research to get a good feel for it. But remember this is a major war zone, and there is a lot of stuff sitting around. Abandoned buildings, abandoned wells, destroyed vehicles, etc. mean it's a complex environment to be randomly pouring cement or dropping grenades at everything you can possibly imagine as a bunker.
A large pile of brush is semi-impassible and fairly easily allows air exchange. A pipe amidst one would be easily overlooked. How about a pipe made to look like a dead tree trunk (complete with open top or large 'rotten' holes? Make it look partly burnt, and a casual observer might not realize smoke wasn't from the tree burning (a smart one would tell by the smell...). A 'rock' made of concrete would only be obvious up-close, and might just seem like someone poured out excess concrete in a pile. A pile of rocks might be big enough to allow air exchange around the rocks.
Then there's the hidden in plain sight stuff. Decorative brick work with openings might not be noticed as an air intake. Or maybe it's the intake for the building it's next to, not a bunker. And why not just fix a smokestack into an actual smokestack of a surface building? I have this picture in my mind of a cabin in the woods with an elderly couple living there, and there always seems to be smoke coming out all the time. An old boarded-up well house without a roof is an air intake, and if you break into it, why there's just a hole in there going down.
The point is, there are as many ways to conceal these things as there are clever people. In most urban environments, most people don't know what every little thing is, and aren't going to be randomly blowing up EVERYTHING unless they are true vandals or are systematically rooting out bunkers. In rural areas, distance and relative lack of reason to suspect bunkers will make finding them unlikely. Bunkers are hard to make, and they usually had a special reason to make one. Most weren't intended to be concealed, but instead to protect from bombing.
So if the enemy controls an area, they'll eventually find a large bunker in operation - the bunker would need regular supplies in any case, so it would be eventually moot. If not, you would have either no reason to look, or be too occupied fighting the guys in front of you and not worrying about a possible secret bunker.
Bunkers were mostly just armored, not hidden. Typically without even a door, as by the time the enemy has reached that far, a mere steel door will barely slow them down much less stop them.
But let's consider the case of a hidden bunker that is not just a tunnel system such as was very common in Vietnam.
These bunkers are huge, and have hundreds of meters of tunnels. There is no reason for the air intake and exhaust to be anywhere near the main complex, they can be many hundreds of meters away, and disguised as other entryways into the ground. Storms drains, water well, etc.
You could reroute the exhaust vent through the apparent chimney of a house out of sight from the bunker location. Even if the house is seen, the presence of smoke from a chimney will not be unusual. Being well off the ground as a chimney should be, there is not reason for the different smoke composition to be smelled from the ground.
Any diesel exhaust can easily be filtered through a basic carbon filter to remove particulates and smell, then run through a bit of water to cool it down, leaving the exhaust appearing as mere cold air from some foul cave.
NO, with even a modicum of effort the air and exhaust from a hidden bunker can be disguised quite well. The same for water source and effluent. (can be stored, if need be). What is more likely to give away a bunker's location are the access roads that were used to construct the bunker, drive away the dug out earth, and bring in supplies and personnel.
And while those cannot be hidden well, as it is very hard to tracelessly vanish a road, they can be trivially disguised as roads leading elsewhere.
If you need to discover a hidden bunker, you need to go high-tech, or patient.
Patience, because inevitably at some point today, or tomorrow, or next week or next month people will enter and exit.
Or high tech, if you are in a hurry. Thermal imaging, as any operating bunker will cause a hot spot in the ground around it.
Or a ground microphone network, which will detect any operating engines, machinery, or clumsy humans inside your bunker.
Hidden bunkers are hard to find, that is why there were still dozens of abandoned WW2 style German bunkers being discovered all over Europe, decades after the war.
And some manned Japanese bunkers that were not discovered until several years after the war! Seems they did not quite get the message that the war was over.
Exhaust fumes or lack of ventilation are unhealthy, but more unhealthy, to the point of lethal, is a bullet in the head/body. I think you are not interpreting the circumstances in the right way.
First of all, soldiers fighting to get control of an area bring with them weapons and rations, not cement. Then, preparing cement requires time for the dry powder to be mixed with water and then poured into the suspected hole. And while doing so, what do you expect, that nobody will shot at the cement mixing guys, just because they are indulging in masonry, not war?
Then, even if they somehow managed to clog the one pipe they found, the baddies behind it would still be alive, armed and hidden, ready to shot at whoever has had fun tampering with their lungs. And maybe they placed the holes in sight of their bunker, just to be sure to get a good sight on the pranksters.
Top this with the obvious countermeasure of creating a lot of dummy ventilation holes, and draw your conclusions: do you better go hunting for the bunker, or do you prefer jamming grenades into holes scattered around a place stuffed with armed soldiers?
Even sparsely populated areas have some population, which will typically live on roads, which are the logical paths of advance for an enemy force. So you can camouflage small bunkers as farm buildings and similar in the small towns along these roads.
Case in point: Constance is a German town that straddles the river Rhine, which along most of its course forms the border to Switzerland. Thus, it forms a natural bridgehead. And during the years before and during World War II, the Swiss were somewhat apprehensive about the Germans invading from this bridgehead. So they encircled it with a ring of infantry bunkers to at least slow the potential German advance. Most of these bunkers are still standing (because they are very well built - the Swiss are good at building for eternity - and correspondingly hard to dismantle). The Verein Festungsgürtel (site only in German) shows these bunkers on a map, and has hiking suggestions.
The infantry bunker, camouflaged as a stone building, is integrated into the town center of Triboltingen. The polygonal "fighting room" was prepared for an infantry gun, a machine gun on a fixed carriage and one observer. The entryway is angled, and the top floor can be reached through an exterior stairway. In the basement, there is a living/sleeping area without an emergency exit.
Edit- here is a nice short YouTube video on the analogue WW2 period bunkers guarding the road from France into Switzerland near Geneva: The Lovely Swiss Villas That Could Destroy An Army.