NiceFill creates a new surface using the same parameters as the surface you're currently landfilling, but without any of the tiles that can be landfilled. For nauvis this means no water or deepwater is generated. It does this so it can figure out exactly which tile it needs to replace the landfill with. I do not yet know of a way to hide surfaces from the remote view, as the remote view is a new feature. I imagine a mod like Factorissimo would have the same issue. Luckily you can't travel to those surfaces without cheating, so it's best to just ignore them.
And that brings us to the other part of the question. Because NiceFill replaces landfill with something that's not landfill, i.e. grass or sand or whatever the tile needs to be, those tiles then cannot be removed again.
Being able to remove landfill is a new feature, and to support it NiceFill would have to create copies of almost every single tile type in the game, so you'd have "Landfill that looks like grass", "Landfill that looks like sand", etc., and use those during landfilling instead. I do have something like that planned for the future, but I first wanted to get the old functionality working for 2.0 and supporting the new planets. Implementing something like this would also take some time, which I unfortunately don't have at the moment.
