The main weather issue is the meltemi winds, which blow from the north or north west, between the Turkish coast & Greek islands, throughout the summer months causing heavy seas. They tend to blow most in the late afternoon ie the return journey from Rhodes. If you get caught by them, the chances are that the hydrofoil cannot "fly", so the journey time is much longer. It has happened to me twice, once late June (journey time doubled) & the 2nd time, in early September last year, when we were about 30 mins late into Fethiye.
I cannot claim that either was the "journey from hell", the first was just mildly uncomfortable. There was, however, a day a few years back, when the waves were so big that many sailing yachts, even those moored in marinas were losing stuff off the decks. I'm not sure that I would have wanted to be on a hydrofoil that day.