If anything, it would be a software incompatibility, but I don't think that's likely to be a huge problem either. AFAIK, light guns/pens don't really have to care about the signal format; the gun/pen contains a photosensor that triggers an interrupt signal to the console, and the interrupt routine grabs the current beam position from the RAMDAC to see where the gun is pointed. In principle this should be mostly independent of refresh rate and certainly independent of color encoding. The compatibility issues with light guns come from displays that don't provide a detectable beam: projectors, projection screens, LCD, plasma, and in fact just about anything other than direct CRT.