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.)