i do lots of hyper-V and NetApp installs, so right up my street! although of course every install is different.
so couple of things, you can use NIC teaming on your Hyper-V host should you wish, however it has to be 3rd party driver driven as Microsoft have no NIC teaming option inherently in Windows Server, this is not Hyper-V specific, this a Windows Server general consideration.
in terms of the back end network, certainly get your SAN traffic on a separate VLAN or physical switch, as you want this separated out.
a 2040 only have 2 ports per controller unfortunately, so a VIF is an option, however splitting this VIF across two switches will be dependent on the switches capability to handle a trunked pair of ports across two separate switches.
what i tend to go for, to rule that out, is to use MCS or ISCSI mutlipath, if you make sure you download the ONTAP DSM this will give you a host more options for how you weight and balance traffic between the multiple 2040 ports, if you install the Windows host utilities kit on each Hyper-V server that would be a bonus for you.
so basically i'd be going for at least 2 ports per server connected to you ISCSI VLAN, using mutlipathing to hit more than one NIC per controller, have each of these connections sat in separate switches to ensure switch resilience.
bear in mind that the LUNS you will try to connect to can only be delivered by one controller at a time, so don't try to have one ISCSI session connecting to one controller and one to the other assuming this will provide resilience, the second controller will only be able to deliver LUNS from those volumes in the instance of a controller failure, when it will take the personality of the failed controller and present all IP addresses and volumes from the failed controller.
make sure you use CSV's as well as this will give you much more flexibility in hyper-v deployement and if you are using System Centre to manage the environment (i'd strongly recommend you did!! :-)) then get Appwatch pro integrated into it as well...allow you a large amount of management control.
hope all that helps, feel free to drop me a line if you want any more detail, happy to help!