NTM particles will cause the surface of water behind them to not appear with some performance mods active. This occurs both with Angelica and with BugTorch, but I believe other mods cause it as well. This is easily reproducable using a drain pipe. Gases have the most noticable effect. Version is 1.0.27_X5091.

Drain pipe releasing steam while Angelica is active:

I have the opposite problem, certain particles, like the ones from the tsar bomba will cause water to be visible through the particles, like xray

Render ordering being broken for transparent objects is a pretty old vanilla bug, especially when water and particles are involved. If performance mods break it even further, then there's not a whole lot I can do about it.