(I realize this thread is a bit old, but it’s the first hit when you google “roon exclude folder”)
Until Roon has an “exclude folders” option.
You could try this: Make an enclosing folder one level above your Roon music folder and put your folder of excluded files in it. So the Roon watch folder and the excluded folder are beside each other in the hierarchy. Put files to be excluded from Roon, but seen by some other server - I’m thinking Squeezeboxsever or daap - in the folder beside Roon’s. Point the server that needs to see the excluded files to the enclosing folder and Roon to the music folder one level down. Assuming both servers see recursively, you should be OK.
I imagine you could temporarily include the excluded folder via a symlink in the Roon folder, thus not causing any disruption to the server pointed at the enclosing folder. I haven’t tried that yet, but it should work.