I have a fair deal of bridge officers. I keep my pool maxed so that I can change my officers to fit the situation. Unfortunately when I change officers I have to go and update my hotkeys. The reason for this is that hotkeys are bound to skills. When I was but Lieutenant I had plenty of hotkeys so every ability could have its own hotkey. I am now a commander flying a science ships and with devices, weapons, and subsystem targeting hotkeyed along with mine and my BO abilities, I have 3 spaces left over. (this poses a different problem best discussed elsewhere) Clearly I can't afford to give each ability its own unique hotkey. Such a system is inefficient anyways since at any one time most of those abilities aren't even active.
Weapon and device hotkeys remain the same even when you reequip your vessel. I think it should be the same with abilities. When you hotkey a bridge officer ability, you shouldn't be hotkeying the actual ability. You should instead be hotkeying that position (ie you don't hotkey High Yield Torpedo I, you Hotkey Tactical officer 1 ensign ability), so when you switch bridge officers the abilities are replaced and your hotkey list remains populated with active skill only. It would make switching so much easier and would help with limited hotkeys slots.