Hard drive fins will NOT slow system fans. the fans run based on box temp, not based on HD temp.
Basically if you put heat generating devices (i.e. more ram, more HDs) then you have more heat to exhaust from the box, but the fins do not reduce the amount of heat.
What they will do is more efficiently remove heat from the drives, making the DRIVES cooler, but that heat is still going into the case and therefore the fans will not run any slower.
I personally didn't have any speed increase in my mac pro and I've got 4 drives stuffed in there. Sounds like something else is going on on your machine.