I am having the same problem, however I haven’t been able to determine the amount of time mt-daapd stays visible.
I find it hard to imagine that it is a firewall problem as I have this:
-I INPUT 1 –source 0/0 –destination 0/0 –jump ACCEPT
in my INPUT chain, So I am accepting all packets. mt-daapd disappears from itunes after a certain period of time, and restarting mt-daapd makes it reappear. I am using avahi, could this be the problem?