Well, looking in the file system for suspicious files (like ~/Settings/Launcher.conf, ~/Settings/Launchersettings.conf, and /opt/QtPalmtop/etc/*), I'm not seeing anything that looks like it controls .desktop files. Personally, I could do without them for files (as opposed to applications, for which they provide a convenient way of launching).
Actually, I hate them. Hate, hate, hate them (Opie developers, please don't take this the wrong way. . . I'm not a C++ programmer, and so I can't submit a patch, and so I really don't have the right to complain--you guys are doing a great job). They are the only reason I don't use the DocTab. I didn't like the DocTab in the original Sharp ROM, but with the combination of the Medium Mount setting, I could see how this would be useful. Regardless, I can't use it because everything is duplicated (more than once sometimes) because of the .desktop files. I wonder if this is a compile-time setting that could be changed in the next build. . .