I generally tape over all "vents"
For example I have vents (for mounting a Fan) that is located back left side. I have two front fans, a High volume rear fan, and a top mounted fan.
The rear fan would pull some air in from the back-left vent holes totally bypassing the GPU and CPU.
What I did is bought a temperature unit (cheapy) with a external wire. Mounted the wire (external sensor) about an inch from the HSF. checked system air temp going into the HSF. Then plugged left back vent holes and checked Air temp going into CPU and cpu temps under load (using prime 95)
Leaving vent holes uncovered and dust - solution is to place a filter material over vent holes - But as I stated, I just tape over.