Foremost, I really like this idea. It adds many many possibilities to the game. Obviously, hiding and ambushes, but also things like system failures. A ship should be able to power down (almost) instantly, which would cause your scanners to not work anymore, so you can't see anything on the radars and your ship is only targetable at close range or not at all, whatever would be preferable balance wise.
So, what happens when your ship is powered down? You'll have no energy, no radar and can't move at all (not even turn).
Concerning what happens when you start it back up, it should either take a while or should be in slow progress, as in .. all of your weapons should be on cooldown for like 5 seconds, your energy core regeneration should be reduced and your speed only slowly comes back up. Cruise speed should be disabled for atleast 10 seconds or until the engines are fully back up.
