Yes and no ...
There are neutral ships but there isn't really a neutral race.
Neutral space is treated by the game engine as unowned by anyone,
rather than as territory owned by the neutrals.
As such, when it generates opponents for missions in neutral territory
it picks your nearest enemy (by closest base IIRC) rather than generating
neutral ships to fight.
Meanwhile, the missions tend to view neutral space as falling into either
the "friendly" or "hostile" categories based on server settings, and never
truly regard the space as neutral. As far as I know, no one has yet managed
to come up with a set of missions that get offered ONLY in neutral space.
Either they also get offered in allied territory or they also get offered
in enemy territory.
dave