I just keep a separate library for my 3D Movies (since I only have a few dozen).
I also add (manually) a small graphic to each of my Movie Posters, so I know it’s the 3D version:

So, for example:

Takes a bit of extra work, but curating my library is one of the things I like about Plex.
[Still have to tell the projector that it’s a 3D Movie coming down the pipe - mine’s not auto-sensing]