Page 31 (in my copy) of mentioned guide describes recommended cabling sequence for multiple HBAs. Nothing stops you using two quad HBAs with single stack, you just will waste 6 ports out of 8 ... it would be HBA 1 port A and HBA 2 port B.
Not that it can't happen....but seeing a slot failure in a NetApp is very real. So, if you have the extra slots and the extra cash, I don't see any technical issues. If I'm short of slots (i.e. want to do 10 GigE, PAM, etc.), I wouldn't have a huge issue with putting my disk off a single SAS HBA especially in a cluster where cluster failover provides some level of protection.
I see this kind of question/scenario as happening fairly often given that the 31x0 line only has 4 slots, no built-in SAS ports, and a single SAS HBA can technicall handle up to 480 disks (i.e. higher than the maximum disks for a 3140).