[ColonelSandersLite]

Honestly, that doesn't really bother me at all.

 

Crew efficiency effects:
sensors (definitely)
reload rates (definitely)
damage control (pretty sure)
gun accuracy (maybe, not really sure tbh)

While theoretically possible to encounter the situation you mention, the only time I don't have any crew in an area is my guns when I don't need them. Technically, you don't need crew in them to use them yourself, but reload rates are atrocious then so that's a kinda pointless distinction. Yes, it's possible to strip a lot of crew out of the sub at port but why would you even actually do that?

On paper, it's possible to have enough casualties that this can be a serious problem. In practice, I doubt it's really possible to survive that anyways.