Has the free space risen dramatically? If not, someone has moved the <3000s into a different folder. ExplorerXP can help discover where. If it has, someone/thing has deleted them -- restore from backups or use recovery software. Mdxterra's idea is a fabulous one, especially if you have an upset employee on the loose.
Viruses need to be discreet to survive, so I'm certain it won't be one.