...I don't want to "thwart" well-laid plans by the PCs, but it seems to kill the entire notion of ship-to-ship classic combat. Given this world has some high-level Pirate Lords, what keeps them all from doing the same, whether it be flying, dimension door, etc.? That's my conundrum: what makes traditional sailing (speed) and weaponry (e.g. the new-age cannons that are popping up) relevant if magic can simply override it?...
I'd advise leaning on traditional weaponry/ingenuity first, then build out your options out as makes sense from there; for example I might comb through cantrips first, consider their use and combine them in flavorful ways with above.
Societies tend to rely on what is simple and effective e.g. The one o'clock cannon to signal time of day (one time) vs. firing a cannon at noon (twelve times).
Chain shot, bolas, nets etc. that can be launched into the air, can handle people flying.
Both Dimension Door and Misty Step have their limits and own effective counters in nonsail scenarios; look to those.







