Let's say the hijackers still see the Twin Towers through the lower visibility and crash the planes into the towers.
If it was heavily raining in New York on 9/11, will the rains be able to help in extinguishing the fires that resulted from the impacts and prevent the heat-induced structural stress that weakened the structures and eventually resulted into the collapse of the Twin Towers?
I would say rain or no rain the towers would still have fallen if the planes hit. That is if the attack even happened with the rain and lower visibility. I would guess they would wait until it was a nice clear day before trying. If however they had to than with the little training they had they would likely hit something else killing far less people.
As for the fires inside the towers I don't see much happening. The fires were inside the rain would do little if anything to them. I saw a video testing would the towers fall due to the fire however I can't find it right now. But it showed that yes the fire would make the beams fail.