You have to remember that both seek time and transfer rate on zip drives are really, really, slow. (29ms and 7.5MB/s, best case, according to specs.) The additional overhead of writing metadata for each file can become significant at those speeds. (Honestly, I'm not sure where metadata is kept in ext2/3. If I'm reading the spec properly, I think it's kept separate from the data blocks.)

Of course, that assumes that he's going to use ext2 on the zip disk. If, for some reason, like so he can read the disk from other OSes, he wants the zip disk to be FAT, doing a file-by-file copy is probably a bad idea, as he'll lose all that metadata, plus have filename issues (the latter of which could be overcome by using VFAT, I suppose). This is actually important to point out, as I'm sure that zip disks still come preformatted, so he'll probably want to reformat it with ext2/3.