As others already said, the reason is that it's not supposed to be used in combat. There are two reasons why reboot & repair exists: First so you have a chance to survive with a 0% module. Second because rebooting your shields would take ages using some of the larger ships. They didn't add it to quickly repair your ship during combat.
If you get shot during reboot your shilds dont come back, if you are moving your shilds dont come back. If during the repair you get shot in the modues, you come back with broken modules still. All these things prevent abuse of the reboot. The three second thing adds 3 seconds to the procedure, of rebooting where you look at the screen for 3 seconds and then press reboot. The tactical option to boost away, turn faoff, then reboot is prety much the closes to a combat reboot you can get and doing so does not give you your Shields back it just jump starts your dead moduels so you can make a break for it or hope you can evade for long enough for your shields to come back natrualy. I cant see how thats a problem as if you have a dead module you need you are going to die unless the other player lets you live, or you manage to reboot in combat using your wits.
Adding 3 seconds to the menue does not realy solve anything and is just anoying. You can do all you could before, granted a little longer and anoying when you are in a pinch.
So if it is to prevent combat reboot it has failed in doing so beyond what was alred in place. It just adds 3 seconds. The macro thing is the only thing i can think of that it changes and i cant see how thats a problem realy eather