Yes, but the zone information for what nodes are available for a given network is stored by a canonical node which speaks the full Zone Information Protocol, as far as I know (I'll have to go and dig out Inside AppleTalk to check). Even though they do not separate traffic (except multicast! which is surprisingly important...) they are still centrally defined objects, not an emergent property of the network.
So, my guess here is when you set a zone name explicitly, netatalk is going "well, nobody else is managing zone names on this network, I'd better do it", and firing up a ZIP listener (??). If you end up with two in this situation, it might break stuff.