Even if the pressure problems could be countered, a bullet hole is likely to leave a pretty ragged profile on the inside of the steel tube. The specification calls for the air bearing skis to ride 0.5 to 1.3mm off the tunnel wall. They'd need to be pretty robust to take hitting the ragged edge of a bullet hole at 700mph.
I think that a bullet hole in the type of tube that supports this much weight is unlikely. Oil pipeline tubes would typically be thinner (less weight to support) and the concept of a bullet piercing those tubes is unlikely.
I wonder - could you line the high-speed part of the tube with half an inch of soft wax or something similar? Then any dents or imperfections caused by bullets would rapidly be smoothed out again, and the damage to the skis would be minimized by vaporizing the wax you hit.
