The Apple online store goes down just for maintenance. I imagine it goes down about every week or so for a couple minutes to back up stuff or refresh the server or something. At my college, the student info server (grades, schedule, etc.) goes down every Sunday morning for the same stuff.
Another explanation to the downtime could be an actual crash of the server (or load balancer, more likely.) The Apple Store runs on Netscape Enterprise 3.6 on Solaris 7, but I don't know the track record for that very well; I assume it must be pretty good if Apple's using it. (BTW: Playboy.com uses the same server software, so it MUST be good, right?)