First, 5Gigs, seems awfully small for a dedicated server. Most companies are offering 20+ Gigs. But no, an OS that takes up 500 megs of space is not unusual.
You are correct shared account do not take the OS into account as part of the quota.
As far as the pop3 boxes go, remember that quota is a maximum value. 3 Megs of space is not "set aside" for each pop user, instead each pop user can pull up to 3 megs from the available space on an as-needed basis. If the pop3 box empty then the disk space is ekpt for general usage. It is very unlikely that all 1000 pop3 users will use all 3 megs at the same time.