I see no reason why a second drive should cause a recuded (reduced ?) air flow - if you take a close look, the smallest opening through which the air must flow is the slot at the base of the front panel - I would expect a second drive to cause a rise in the internal temperature, so that you might detect the air coming out to be warmer than with a single drive.
If you want to verify the fan is functional, remove the front cover and restart the unit - during the boot process it will run the fan up to full rpm and it will be both audible and visible (through the disk slots)
Depending on the disks used and the actual usage of the storage, you'll probably find that the fans run at different times, they will turn on, off and change speed as dictated by the internal temperature changes, so as long as the fan runs during the boot process I would not be too worried about it not being on at any other time.