Dunno. I would fear that the removal of blocks in/under water would cause blockupdates in the large nearby area of water, despite there being visual changes in the water or not. And it is these that are a resource hog for the server. Also don't think we should confuse it with the massive fps drops we can get with the changes in flowing water and the resulting light level changes.I... have no idea how the EnderQuarry handles liquids. But, since it mines straight down, rather than layer by layer like the BC quarry, I'd be surprised if it caused anywhere near as much lag as the flooded BC quarries people used back in the days before auto-pumping quarries.
But not really that well acquainted with the mechanics of it. Just know that block updates it fluids is bad