Well you've not really given us a great deal of information and your question's a bit vague but if the question was 'how will the iSCSI work on a 2k extender compared to going directly into a 5k' then it depends on where your servers are. If they're connected to the 2k directly then there's little difference but if the servers are connected to the 5k (or further down that chain) then obviously you'll be introducing some, small, degree of latency as the SAN's further away. If I'm misunderstood your question then please come back with more detail and/or clarifications.
By the way an iSCSI network is still really a VLAN, as it uses a LAN-protocol, if it was FCoE or FC then it'd be a VSAN, sorry to be picky ;)