This happens all the time with companies which don't use / can't afford to have their site hosted on more than machine. Assuming you use Windows on your own machine, you'll be familiar with the concept of having to reboot your machine after Windows update has run, or after installing "big" software. Web servers are no different...
Generally speaking, if a site is down for more than about 10 minutes, it might be experiencing problems. Less than that means that it's probably just installing updates...