Hmmm, just updated everything and tested it on my side, and biter nests still exist for me.
When you say you're running with "this full mod set", do you mean, just the mandatory planets and nothing optional, or do you mean all of the mandatory AND optional planets (or including unlisted planets, I've fallen behind on a couple of them recently)?
If you are running with ONLY the mandatory planets, then I have to wonder if you maybe generated with biters disabled? Alternatively, there is some non-planet mod preventing them from spawning in, because enemies appeared as normal for me when starting on Nauvis (I also haven't tested Any Planet Start or non-default settings for any of the planets, that could also make a difference)