If both the Excel file and the word documents were on your desktop to begin with you should be able to move them anywhere as long as they remain in the same directory.
If they aren't in the same directory it might be more difficult but should be workable provided you create a similar directory structure on the target machine.
I used to have that problem with hyperlinks but I don't seem to have it anymore. I'm not sure if I upgraded excel (working with 2003 now) or if it has something to do with how the hyperlinks are set. Or maybe there's some option I found that I don't remember.
If the files use some sort of standard naming convention, you could just write a macro to reset all the hyperlinks after you move the files. If not, you might be able to write a macro to read all the hyperlinks before you move the files then use that info to reset the hyperlinks after the move.