Onboard your own ship is obviously
the least likely place to be shot and disabled/killed. I don't think any large percentage of the crew would wear armor - even ship's security is gonna be pretty lightly equipped. They're more like MPs than infantry.
It remains a good idea to keep armor in stock. The people you send down to an uncharted planet could be headed into a warzone or an ambush for all you know. And in the event your ship is
boarded by armed belligerents, you can minimize your own casualties by issuing the good stuff to your security personnel.