AFAIK, it simply disables the duplicates by switching them "off" (what the rules for that are, I don't know, but in the case of Classic fonts, they are generally older versions and they are the ones that get disabled). They are not deleted or moved from their font folder at all and I think the "off" status simply prevents them from being registered as active by the ATServer (Apple Type Server) process. What this means is that anything that doesn't use ATServer (e.g. any app running in Classic) will not be affected if you resolve duplicates. In other words, it is safe to disable any fonts located in the Classic system folder with zero impact on either apps running in Classic or apps running natively in OSX (other than preventing any potential problems in OS X due to the presence of duplicates, of course!). Personally, I resolve the duplicates myself to make sure that the versions that are disabled are indeed the Classic ones, and not the up-to-date OS X ones.
A question remains, though - why don't Apple ship OS X with the Classic fonts disabled in Font Book by default as it doesn't seem to cause any problems, and potentially prevents some from happening?