Can bad weather stop Santa from flying?
Yes, it certainly can.
Santa is subject to the weather just like the rest of us. A bad storm for us is a bad storm for Santa.
That is why Santa has a Weather Department, so he can know what weather is coming and how to get around really bad storms. Santa might, if it is a small storm, fly right through it. But he does not want to put himself or the reindeer into any kind of danger so if a storm is really bad he will just fly around it or over it.