Well, I've just gotten the game about a month ago. In my first game I played insane sized map, cause well space is huge. Also I tend to like tight clusters. Anyway, here's how I found to manage the number of starbases.

1. During the initial phases, micro managing each starbase is possible. 

2. Once you get to the control of 4 or more clusters worth of planets and resources things get complicated. Stick to building the starbase and not add any additional upgrades. This works great for pragmatic races as they get more bang for their buck than benevolent factions. If you need more of a resource, go claim new ones rather than further develop the old ones. The exception to this is precursor artifacts. Those should be maxed out as soon as possible.  Do not worry if the starbases seem defenseless (the base stats are good enough for small groups of pirates), as even heavily upgraded with weapons, shields and armor, they can still be taken out by a heavily armed fleet with ease. It's a nice to have, but for all intents and purposes not worth the effort management wise. 

3. If at peace and your navy is sufficiaent to deter agreession, got through and have each starbase request 15-20 constructors. (Less if they were part of the initially micromanged group).

This worked for me in my last game and did cause me to feel like I was devoting to much time to the starbases.