If you look in the Gamepro database, under the title and issue number for each issue is a status marker. It may say "preserved," meaning it is available for download, or it may say "scanning" or "editing" meaning it is in the process of being added to the site. If it says "not allowed," then it can't be added to the site, usually because of our cut-off date, but sometimes because the publisher has requested that we not share their magazines.
For the GamePro issues from Jan 2002- Dec.2006, it will say either "missing" or "acquired". "Acquired" means that one of our scanners owns that magazine, and it may (someday) be scanned and added to the site (although not all of our scanners mark the mags they own). "Missing" means that either no one owns it, or those who do have no plans to scan it anytime soon.
So the lack of GamePro post-2001 is simply because no one has scanned any of those issues yet. If you'd like to contribute, you're welcome to scan any of the issues up through Dec. 2006. We have very few people actually doing the work of contributing scans to the site, so we'd greatly appreciate the help!