Hiding a selection just hides it from the view so it doesn't get in the way while you're editing the rest of the ship. Once it's exported to .mod, it unhides automatically so if you were to re-import the ship, everything would be back. If you want to get rid of it, you should just delete it entirely (but keep a backup just in case).
The ship can have every HP number you can think of but only the ones in the UI will be used. Some UIs use a set of hardpoints while ignoring the rest. If you put a weapon on an unlisted HP that's on the model, it should still fire in-game. You won't be able to access or repair that particular one though.