SRM doesn't care about VM-FEX vs. non-VM FEX. Are you using NetApp replication or vSphere Replication? As long as your VMs are replicated, and you've successfully run some SRM Recovery Plan tests you should be fine.
Just to be clear, your hosts are using iSCSI, right? As compared with connecting iSCSI storage directly to your VM guests? iSCSI to hosts will just work (assuming correct SRAs, etc), iSCSI direct attached to VMs requires the iSCSI storage be presented the exact same way at the recovery site so that when the VM starts the LUN is just "there"
Hope this helps