Playing around vanilla, I have to say even the game itself is unstable regarding "entities" (npc, vehicles etc)... I brought a stolen chart up to saint denis, dismounted, walked literally 6 steps in a direction because two dude were screaming, looked behind me and the chart was already gone.
Same with random encounters, kill a bunch of people, chase one of em for 15/20 meters, turn back and the bodies already disappeared - to not talk about random bonfires, sometimes you follow the smoke and it disappears along the camp while you're almost there.
I think this means the game is at its limit anyway and they put some sort of flush algorithm like that to prevent it from going bonkers, so probably that's why any mod whatsoever can clog the engine and it starts despawning active entities to prevent memory crashes etc...
I think our best hope is if Rockstar will release the "next gen" updated they promised, that will probably make the game stable in that regard....