What do you mean magical energy doesn't transfer well through water? Waver found them because of trace magic in the water coming from the sewers.
And it was still there to be detected and not all downstream wasn't it? It doesn't
transfer through water, for a variety of reasons starting with water isn't a good conductor (if you're now wondering about electricity, it mostly travels over the surface of water, it takes a direst lightning strike for it to get any real depth). An example is heat, most of any body of water's heat is stuck within a foot of the surface, and the rest doesn't get much farther than that. And magical energy that leaks into the water won't go anywhere until the water does, it won't just spread through the water.
Actually, both in canon, and in this story, there have been MULTIPLE instances of the Archers making shots while moving. Especially at the range they were? Hell, an average person can make that kind of shot. They DID make those kinds of shots as before canons became a thing, people were using bows and arrows in ship-to-ship warfare. People make these kinds of shots on horseback.
The important part of my post was the 'relatively still' since absolute movement doesn't matter as much as relative movement. The other important part is that they are in the middle of a magical hurricane. You're talking about what they can accomplish in ideal conditions that don't exist. Also, until the modern era, bows weren't made to be precise in warfare, as much they were meant to hit something at a distance. Honestly we don't see the Archers making any shot that are a tenth the difficulty of the ones you're proposing. And is Revenge even in Emiyas range, you can see for a far longer distance than we know Emiya can reliably hit a target on the open ocean. You are severely underestimating the difficulty of the feat you are proposing.
They wouldn't have all just simply focused on Blackbeard's boat solely. They should also have been paying attention to their surroundings as well.
Yes, they weren't just focused on Revenge, they were also focused on Bellamy and Jones. Where else would they have focused? Drake is focused on what's around them so it's not like they'll be able to help in way keeping watch. This is like complaining that someone getting sucker punched from behind (IN A HURRICANE) should have seen it coming somehow,
you're certainly not going to bother explaining how, just that they should have somehow predicted it. Maybe the fact that the only one of them there experienced in naval battles is Drake, and to the rest of them, all the ocean around them is full of absolutely nothing? Seriously, why should they have been looking in the opposite direction of the three actual threats to keep watch on a vast expanse of stormy seas for the possibility that someone might come from that direction?
Stop acting like they're perfect individuals in ideal conditions with vast hoards of experience to draw upon for this exact situation and an omniscient perspective that automatically understands what everything around them is doing, why, and the effects of those actions.
The only reason you can say that any of what you think they should have done is easy, obvious or the best situation is because you're here reading it, and not actually in that situation. If they had actually tried any of that, things would have been worse. Maybe you're just reading too many Mary Sues that you're used to the plot bending over backward for the MCs? Hindsight is 20/20, and foresight is myopic.