Two things to consider. First, the fact that you are using two different frequencies is only relevant if you have configured networking in such a way that 2.4GHz is one network, and 5GHz is another network. Otherwise the fact that you are using two different frequencies is like having a cable connection and a WiFi connection. Cabled and wireless networks can still see each other if they are in the same LOGICAL network.
Second, iTunes uses Bonjour (as does the speaker function on the AirPort Express). The only time you will run into these devices not being able to see each other is if they are on a separate logical network (VLAN, VPN, routed, etc...). JUST being on two different frequencies in WiFi does NOT put them on a separate logical network.