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The crew are surgically altered before launch to have larger internal cavities for waste storage. They no longer have urgent needs to go to the bathroom and can stay on duty for as many days as modern future drugs can keep them awake. Waste evacuation can happen whenever the plot needs them to leave their stations for other purposes.

The crew are surgically altered to connect their insides to their outsides [WARNING, PSYCHOLOGICALLY ICKY, BUT NOT ACTUALLY GORY]. When necessary, they can 'plumb in' to a drainage system. Human precedent exists, and that's because I don't want to link or consider the genuine human precedent.

Part of the spaceship exists in subspace, hyperspace, another dimension, a phase shift. But not the left half or the right half or the top half - the bottom half. People below the waist, their feet, the floor, are out of sight, out of smell and out of mind.

People have iPads gone mad. They do need bathroom breaks but it doesn't mean they abandon their duties mid fight, since the duties can be brought to the bathroom with them. Holoportation so the crew still see them sitting at their original posts is an optional extra.

The crew doesn't eat. Like Sam Rockwell in the film Moon, there are endless clones. They wake up, live until they die of dehydration, are disposed of and replaced with a clone. No food, no bathroom break. Very Matrix as well. This point has the advantage that it fits your "no bathroom breaks" clause to the letter, while not fitting the spirit of "no interruptions to a long situation", which is a perfect nitpick ;)

The crew doesn't eat, but for a much more mundane handwavy reason: nanobots. Yes, their bodies contain more nano than an entire series of Mork and Mindy, and that fixes the problem. How, you ask? Shutup, are you saying there's a problem nanotechnology can't fix? Do you wanna fight?

They are Borg-style human brains but supported and animated by non-biological matter. Cyborgs, robo-bodies, mechanical life support systems, they're not really people at all. Before launch their bodies are put into suspended animation. Electric life is introduced, it runs in the pre-existing neurological patterns in their brains, like a tram following a human-behaviour-shaped tramline. Shadow humans mimicking the bodies they exist in; stasis-bodies have no muscle control, but they can be animated by the ship's internal tractor beams like a futuristic stop-motion. From the outside, you'd never know the difference.

Wow, did you say no bathroom breaks? Because I totally didn't just go to the bathroom. You can tell that I didn't go just then, because no time passed between when I was just here, and when I am still here so there isn't even a 'then' for you to be referring to.