I had a friend a few years ago who went by
Nova, because her last name was Cassanova. So I immediately find it feminine - I think it's the -a ending, perhaps, combined with the association.
It's out there, and not quite my style, but I wouldn't necessarily *mind* it on a boy, per se. I think it's hard to find the right pattern, flow, and sound for middle names and combos when the first name is short and ends in -a.
Nova Morgan almost sounds a little sing song-y in my head. The pattern of it seems to fit more as a middle name in my head.
Nova SamuelNova LeanderNova LennonNova MichaelNova MaxwellNova RichardNova StephenNova Vincent
Or, in the middle name spot:
William NovaMichael NovaAndrew NovaDavid NovaArmand NovaAlexander Nova(Xander or Xan?)
Vincent Nova