I think
Morthoron makes some good points. Consider, Ulmo himself could probably wipe out the entire armada with a tidal wave.
But regarding the authority of the Valar. The Numenoreans are a special case of Human in Middle Earth. Having just reread LotR (for the 6th time

), I was struck by how many times and ways Tolkien makes this point, be it in reference to Aragorn, to the Dunedain of the north, or to Imrahil and is kin from Dol Amroth. All of this to say that the Numenoreans were not typical of all men. The Valar themselves were the givers of Numenor to the Dunedain (correct me if I'm wrong). This placed them in a somewhat trickier (dicier?) position in regard to their authority vis a vi Iluvatar's. Therefore, the Valar did have some right relative to the land on which the Numenoreans dwelt. Nevertheless, these still were Children of Iluvatar. So the Valar had, one could say, a tight little ethical bind to figure they're way through. Instead of make a wrong choice, they made the best choice and deferred the matter to Iluvatar.