It can break custom hacks that expect specific usernames or userids; also, for example, the tables userfield, post, thread, privatemessage, mailmessage, mailfilter, mailfolder, mailab, etc.
edit: stock vB doesn't have a problem (except when just deleting a row from the user table), but hacked vBs, which many people, including myself run, don't always integrate with vB's user deletion system. So you're fine if you want to use stock vB