My skinatra won't autocast the nanites, even if friendly craft in the radius have hull damage. If I set scramble bombers to autocast, it DOES autocast it but not how I would expect. It autocasts it occasionally, but if it has remaining antimatter when the cooldown ends it won't do it.
I was invading the pirate base with a pair of skinatras, they both failed to autocast nanites and once the fleet was dead and I wanted them to spam bombers to kill the turrets, they failed to execute the skill multiple times in quick succession, despite having 150+ antimatter.