When this bunker (in its AI car form - AAI Vehicles) is out of either fuel or ammo and gets attacked by explosive spitters from the explosive biters mod, my UPS just goes from 60 to 10.

Uhm
I did some testing myself, and I couldn't reproduce the issue you mentioned (empty bunker creating lag).
What I noticed however is that if large amounts of those biters explode at once, it creates a lot of lag due to the many explosions and fires. But that has nothing to do with my mod.
So either you can come up with some more evidence and I can investigate more or ig thats the reason ¯\_(ツ)_/¯

UPS falls when the bunker (AAI) takes damage from a large number of enemies.

Yeah noticed it too now on a busy map. I can just guess that the reason is that attacked AAI vehicles get pushed back and the bunker can't be.
And since I have a turret version of the bunker anyway, pls just refrain from using it in combination with AAI. Aka use the turret instead of the car-with-ai version. The recipe to make the AAI version has been hidden now and the tech doesn't unlock it too. Users also get a message when updating their save file to the newest version.