They can force a reboot, but that still keeps it offline until the end of the next Combat Turn - which, for a vehicle in motion (a helicopter especially) is an eternity. Otherwise, the cycle is as long as you want it to be.
As for Format Device, it would work, but if it's locally piloted (the only time it wouldn't be easier to just go for Reboot Device, since you have to do that for Format to work anyways) it wouldn't matter - it can't be accessed from the Matrix, but it can still be used through normal physical means. So, what's keeping a decker from doing that is the fact that it actually has somewhat limited usefulness overall.
And are we talking about a human manually piloting it, piloting via AR locally or remotely, or being jumped in locally or remotely?