It's certainly an interesting idea, but how about the tool only works when the armour is down, so you can access the ship's integrity underneath? Using it on the armour component while the armour is up would remove armour.
I mean, that'd make it more balanced in my opinion, but it'd open a floodgate of trolling opportunities. There's the problem with that.
Also, perhaps there is perma-perma? You can only repair the hull to a maximum of 50%, that way you will still die to a single heavy flak or quick enough that tanking is unlikely to save you from the mortar. It might, however, be very useful for ships in the hull-break-equals-guaranteed-death zone.