Yeah, if you build a waypoint ON the starbase, then set the planet to send new ships to the waypoint it will marginally semi-automate itself, but yes, you have to do every upgrade individually.
It's a bit of a chore, but it's balancing that way. Starbases can become just ludicrously powerful, and you don't want them to get there too fast. I've yet to have a single game in which I've completely upgraded a starbase to its maximum potential.
Ofcourse, figure out what you want to use the starbase for, then focus on that. If a starbase is there to boost your economy, there's not a lot of point to putting 15 weapons upgrades on it. I typically do a few, then some shields, and leave it at that.
A military starbase, however, you want to build as tough as you can.
Creston