Some work on further optimization is underway, but they are more about algorithms than the number of entities. So it doesn't look like a solution to your situation
On the current saves I have 50-60 ups (one of them is a K2 deathworld marathon, where the base is completely surrounded by nests)
If you can link your save, I think I can take into account the situation in the new versions.
I'm sure that something will be able to come up with, but a new version is planned in about 1-2 weeks
upd: Also, the fixed version already has overpopulation control (max: 60 nests per chunck), so it would be doubly interesting to find out what's going on there.