Uninstalling the game doesn't remove mods. Unsubscribing from them would remove it as long as you have the steam client open in the background and the game not running, but something could have happened.
Either way you can just go to the launcher Mods tab and disable mods by dragging them back to the left panel from the right and then the game won't try to load them.

Thank you very much for the answer, I'll keep that in mind for later.
The mod didn't show in the mods panel either that was the strangest part before reinstalling.
A few minutes after I posted I checked again and found that somehow the Regrowable seeds mod was subscribed to again even after unsubscribing and deleting and reinstalling the game without being subscribed to any mods. After reinstalling the game only the problematic folder existed, I checked my subscribtions and found that one mod there again. I unsubscribed from regrowable seeds again and now it seems to have removed the folder. Still strange as regrowable seeds had it's own .pak as I recall, but I dare not subscribe to it again to check as now the problem seems to be solved (hopefully).
Never had such a thing happen while modding games through steam - I hope I won't encounter such a problem anymore.

Yes, that's the mod you mentioned in the initial post (1388522920) so it's most likely that mod and it simply has a .pak file with a different name, which is not uncommon.

In any case you glad you solved it and no need to worry about stuff like this, since you can sort it out anyway. Most likely what happened is that the game didn't finish closing properly when you pressed unsubscribe so the file was still in use or something.