The OS9 and OS8.1+ Finders do not support long filenames (OS8.0 doesn't support HFS+ at all, so that point's moot). Therefore, long filenames will be truncated when viewed there, using a # followed by strange four-number string (perhaps a checksum or hash?).
However, any System that supports HFS+ should also support long filenames, even if you can't see them in the Finder. Look at CrushFTP for an example of a Java app with long filename support in OS8 and OS9. In other words, I think you're in luck.