List of things that get vacuum wave that matter:
Mew
Blaziken
Infernape
Lucario
Toxicroak
... yes, they do get Vacuum Wave, but how many of them commonly use it? Let's check the statistics (I like statistics):
Mew: appears on 1,39% of all teams and carries Vacuum Wave around 2,5% of the time. Not something to worry about. (Wow, Mew is surprisingly unpopular.)
Blaziken: Vacuum Wave is a tutor move - as such, it's incompatible with Speed Bost and practically never used.
Infernape: appears on 3.89% of all teams and carries Vacuum Wave around 5,5% of the time. I suppose this could pose a problem to Dory, but it's rather unlikely.
Lucario: the most problematic of the bunch. Vacuum Wave on Luke is pretty common this gen, it seems, and Lucario itself isn't that uncommon (being on 3,68% of all teams) compared to many other pokémon.
Toxicroak: again, Vacuum Wave is seen fairly often on it, sometimes even with a Balloon, but it's only actually used on 1,6% of all teams.
... in other words, Doryuuzu will rarely need to worry about these, unless you're trying to come up with a set that specifically counters Iron Defense Dory, which I doubt.