Yes, iSCSI works across any TCP/IP connection, along with other TCP/IP traffic.
If you were to use ATA over Ethernet instead, that NIC would be dedicated to only disk traffic.
As far as I know, you can get any internal ethernet cards for your blades, and they will work with any ethernet router modules for the 3,4 network module slots. You may want to ask your IBM sales rep to be certain.
From what I've read, the only difference is that you want the flavors to match... don't get Infiniband network modules for Ethernet CFF cards, or the other way around.
You will need networking modules in slot 3 of your BladeCenter chassis if you want one additional blade-internal SFF or CFF network cards to function, and you will also need a networking module in the fourth slot if you want two additional internal cards to function.
Does this answer your question?
Disclaimer: I own a used BladeCenter E chassis, and thus all of my information comes from reading the docs, I've never had any contact with IBM support.