I'm following this topic for a while now and started doing some testing of my own. Mostly I did some tests with only a few .asi mods, including one that I'm working on to see if any of them break the animals/ped spawns or trains. So far peds and animals seem fine. Today I added whyems dlc, and peds/animals trams (4~6 passengers) seem ok. I found this native here on the db _GET_NUM_FREE_SLOTS_IN_PED_POOL () //0x313778EDCA9158E2. So far the lowest value this has returned me was 8, never reaching 0. I don't know if this is of any use though, since I don't have previous exp modding R* games, and I'm not yet familiarized whith the game's engine.
One thing I have yet to test more in depth with my current game and mod list is the trains. I plan on doing that tomorrow if I get the time. Also I'll try to do some more research online to see if I find any info on how the game engine works with handling scripts, pools, memory etc.
I'm also going to take a look at Rampage trainer, to see if I can get any useful info about what the F is going on.
Oh, btw. I kept adding mods during my playthrough and never noticed any of these issues until I accidentally stumbled upon this thread.