radon mitigation fan running, but u-tube manometer shows no pressure differential
Our u-tube shows a 2" WC.  IMO, the hole is the problem: the pump is sucking air from the basement, making both sides of the tube at the same (basement) pressure.  Hence, 0 pressure difference.  This will obviously reduce the suction from the subsoil; at the same time, it will be pulling radon-contaminated air from the basement.  I have no idea what the net effect would be.

You could get a continuous radon monitor.  (Amazon, $130)  Not cheap, but I find ours very reassuring.  

FYI, a couple of things, from experience with our system.  (It doesn't seem like these apply to your problem, but just in case.)


We've had the outlet ice up in winter.  (Moist air from sump, cold pipe.)  When this happened, we showed 0 pressure.  
We've had problems in summer, where a water bubble developed in the u-tube.  This affected the reading, but I don't remember how much.  At the time, we were drawing outside air into the basement, and getting a lot of condensation.  So, warm air, u-tube in contact with the cold pipe.  We now keep the cellar mostly closed in summer, and I spaced the tube out from the pipe.