I opened Riley's Story neighbourhood in SimPE and I found a lot of carpool drivers.
If I look into the Riley's Story neighbourhood in Program Flies there are only 3 carpool drivers like other Maxis default neighbourhoods.

The same happened in Vincent's Story neighbourhood too.
There were hundread of carpool drivers.

Why is the game creating new carpool drivers instead of using the old ones?

Have you tried using anti-redundancy mods from MATY? Not quite sure which ones to use because there are just so many of them. But look for the NPC one.

I already have the antiredundancy mod installed.
It is the OFB version.

It still generates new carpool drivers.
Should I get the base game version?

Are there any other mods which prevent spawning NPCs?

I still have those issues.
It seems like it is only active during the story.
I haven't checked it after the story...

You should definitely see and check if it's appearing outside of story mode. I don't think it's safe to play the story mode with mods. (Once, I was playing the CS story mode with (I believe) Boiling Oil's No Sim Loaded hack. A few chapters from the beginning were fine, but once I reached Rhinehart, he just stood there and the story stopped. Once I'd taken out the mods, the game continued as usual.)