I think they already do. I have added mods after a game has started and when I load the game again, the mod still isn't available. But, when I start a new game, the mod is available.

I only found out after I'd deactivated the Charcoal Burner mod and then loaded an old save by mistake instead of starting a new game (half asleep at the time). The mod was still active in the loaded game and the Charcoal Burner was still happily making Charcoal.