Your construction characteristic and culture bonuses do apply to space based yards. But the advanced racial trait does not and they get no population bonuses.
Planetary based are faster individually, space based though allows a greater overall rate with the same number of planets because you can have as many as the game will allow you to build bases. Plus it's nice to have several bases over one planet and be able to produce a fleet in one spot rather than have to collect all your ships from all over the empire.
It all depends on your play style. Personally I use both.
Geoschmo