When flying over water via mech armor (or the "All armors can fly" mod), the swimming effect still happens, despite the fact it shouldn't.

That is because flying isn't truly a thing. The character is still on the water tiles. I have no plans to change this or add detection of flying since this is done differently with different mods and I'm not sure this is even possible to do without having to update it for every new or changed mod that has flying or boating.

Well, could you update the description to say something about "visual bugs that won't be fixed, so don't ask" section with the whole flying part causing splashes?

You can see it as hovering just above the water. You will then still have splashes and ripples.

Makes sense. Sorry for any bother.