While it is inconsistent, I actually like it.  It's a very easy way to remember which systems have starbases and which don't; the starbase systems stand out this way.  My bigger complaint is that with hangar defenses you can select the fighter/bomber makeup BEFORE the hangar is built (i.e., do it when you queue the building), but with starbases you have to wait until after the hangar upgrade is complete before selecting.  It's annoying to have to go back through each base's system to make sure I remembered to allocate its strike craft, and on more than one occasion I had a starbase fight off an enemy fleet with the strike craft unallocated.

Absolutely, I'd love a dedicated icon of some kind for starbases.  Put them at the top of the "ship" bars on the left and right, for instance, with a distinct color...

And I don't build hangars on most of my bases any more.  I did at first, but even at 4 squadrons per slot, it's just not worth it when compared to the weapon/health upgrades, deflector shields, etc., all of which have far greater utility.  (Of course, I play Vasari; the TEC and Advent players might have more need for something that can reach out and hit a scout trying to sneak around the edge of the well).