-I know next to nothing of airships, but I believe your problem would be controlled flight; a huge airship has huge drag and once winds pick up, you'll soon run out of engine power to counter that drag - and all of a sudden you find yourself going the way the wind blows, which may or may not be where you intended to go...
(Presumably that same drag will cause problems for the structural integrity of the airship, too.)
I suppose winds will be the major problem for very big airships, but I believe there are lots of ways to deal with it. Using the wind in sailing is a known art. There could be technics to counter that? Or cruise along the wind and take a slightly different route. Or in general, probably you will have to take the winds into account a lot more, when planning blimps routes. And the winds are also different at different altitude.
And above a certain height, >10000 m, it is usually much calmer, but I think ordinary blimps cannot go that high. Different outside pressure etc.
Possible to mitigate with adjusting the amount of hydrogen by compressing/releasing?
(Presumably that same drag will cause problems for the structural integrity of the airship, too.)