Yep, I was doing the same task as you and the first thought was to use that 'if' check inside hotspots, but it was not simple. I made a test then and added two hotspots into first pano of the tour (one with webvr.isenabled == true and one with false) to see how it works and there were issues and Krpano works very logical here, the only thing is to understand its behaviour:
1) First pano is loaded before the VR plugin (it seemed so to me), so inside first pano none of the two spots were visible initially. That is, "if" check works only when xml is being parsed, so for Krpano there were no hotspots in this case (I used normal panos).
2) If I go from first scene to second and then return back, I see the spot with 'webvr.isenabled == false". If I enter VR then, the same spot stays visible. The reason here is that normal pano is not being reloaded when entering VR (Multires ones are reloaded to use webvr-ready images).
3) This is all quite logical, because "if" check inside attributes is meant only for xml parsing check - Krpano goes thtough xml at startup and checks those 'ifs' to see which elements are needed and which are not.
All this is based on my tests and experience, maybe Klaus and other guys here may add something about it.