Then why are crew members taking theirs off on the ship?

Ask the devs. Ships aren’t settlements, I guess. They take their space suits off on habitable planets, but you still keep yours on. If you go to the helmet section the toggle says “breathable areas.” It’s not a bug, just a weird decision.

I mean that the bar didn’t fill up at some point no matter how much I blasted them.

I don’t know what that means. There isn’t a bar to fill up, you just shoot them to “death.”