You neglect the friction that even laminar flow would experience while flowing into the tube.
If you make small fins at the top of the tube you can even exagerate the effect and introduce turbulence, which further reduces flow rate.
There is a reason why pipelines need pumping stations every couple miles, to keep the fluid at speed.
Sure the wave might propagate at the speed of sound but that doesn't matter much if its pressure gradient is slow enough.
https://en.m.wikipedia.org/wiki/Hagen–Poiseuille_equation#Po...
Edit:
To give a good analogy:
Electricity also travels at the speed of light through a cable, however due to resistance you will get different current reading depending on where you measure.
Edit2:
I reread your argument, and there is also a flaw in your energy calculation.
The energy per time is not proportional to the length of the tunnel, but proportional to the size of the inlet.
Your calculation would be if you remove the entire top of the tunnel at once, over it's entire length.