Okay, I solved it myself.
Just come on, everyone can say delete the mods, delete the cashes, make a new save file, etc... It's so common and useless advise, usually everyone tries it before asking, you know?
I totally re-installed the game,
ran with no cc, no script mod except the all cheat mod (to skip the storyline).
Here are the results:
1. A whole new game : successfully removed the bothersome cloud.
2. Gameplay with some mods, ccs : nope, no problem.
3. Gameplay with a script mod : perfectly working.
4. Gameplay with my old family : The cloud is there, the weird plants remains.
5. With a new game I merged my old family with the new sim, not just simply replacing it (I don't know how to say it in English properly) : no glitch occurred.
6. Same circumstance, but used the old lot I made when I was playing Strangerville before : the game was perfect.
So something was in my old household, yet I don't know what's the problem.
Or maybe you must make a brand new household when you are playing Strangerville, not just simply using your old household in your gallery.
WHAT THE HELL OF A GLITCH IS THIS? I don't understand.
Thank god and my free time now I can replay the Strangerville with my favorite household and my favorite house lot I made before, not just simply restarting all things over.
Does anyone can replicate this?
I was able to replicate this, well, by accident anyways.
A long time after finishing the quest, I had a family request maximum strangeness, followed by normality. The ensuing result was normalcy, with the plants everywhere. 
Wow, didn't realize this was a bug :D Well, you still have "strange fruits" and you can plant them or get other sims infected by them, so plants still growing (kinda, they grow slowly and usually start growing anew after each reload) is not a bug. But I agree the cloud shouldn't be there.
Why this is marked as "solved"? Because it's not.
