Are you talking about a "inc" directory (ie. non-vBulletin) or "includes"?
If they managed to change a file, then most likely your hosting account (or if on a shared server with bad security another account on the same server) is compromised. I striongly suggest that you ask your host to find the reason as they might be able to do it again any day.
Finally you can not crack a MD5 hash. For plain MD5 there are some rainbow tables around providing a way to lookup hashes and their possible plaintext value, but i have never seen it done for mutliple MD5's like vBulletin is using and i strongly doubt anyone will ever make such tables.
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