Magellan is a bad example because it has an option for max. filename length. Older versions of DOpus might not. Workbench can be changed to long file names since 3.5 IIRC.
However, it's dangerous to set Workbench and the like to long file names and using a file system which cuts names off after 30 characters. For example let's imagine that "long_filename" becomes "long_file" and "long_filename.info" becomes "long_file", too, then the icon will overwrite the actual file. So be carefull to tell your copy program the real max. file name length the file system can handle.