2 repair bays are no less effective than the repair bay spam i have seen as long as you have antimatter... however... you dont have the redundancy if one dies. Having ONE hanger defence for advent surrounded by repair bays are MUCH more effective than 3 more repair bays... and if you manage to fit in an antimatter recharger... (or a few disciples) or for tec... just culture... vasari dont get a break.
Either way... Hanger defence > hanger upgrade on starbase