Anything moving through the air, even at infinite speed, is bound to create sonic waves of some sort, eventually.
A ship warping through may hit the air too quickly for any conventional compression to take place - perhaps the deflectors just punch an "applecore" of air out of the atmosphere, without disturbing the air molecules outside the "core" in the slightest. But there'll still be a thunderclap from the filling of the hole with surrounding air, as nature abhors a vacuum (and isn't very fond of leafblowers, either). Not exactly like a sonic boom in its mechanisms of birth and propagation, but the effects would be more or less indistinguishable by a single observer on the ground.
Timo Saloniemi