I agree. This was just one of a number of surprising things left out of the design. Among others, the hard-drive interface which means that an external firewire drive can transfer quite a lot faster than the built in drive, the need for a riser card for bluetooth and Airport Extreme as opposed to just putting the slots onto the mainboard, and the not-so-easy-to-open casing, which goes against Apple's current push towards cases that are easy to open and exchange parts on.
Still, the ommission of optical out, as featured on the iMac and Airport Express, is a really odd oversight. I always assumed they did that to actually sell more Airport Express units to Mac Mini owners down the road.
That said, there are third party Firewire connected 5.1 digital output boxes, that you could use to connect to your home theatre.