The fact that they don't completely submerge, but skim the surface, makes them difficult to track using our undersea surveilance equipment. When the diesels are running a submerged sub makes a distinct sound unlike an identical engine running at the surface. The sounds get diffused in the ambient noise of the ocean surface and make these things look like any other pig boat.
If they were to submerge and run even at a shallow depth, the sound signature would be more defined, less diffused identifying them as threat targets much more easily. The Navy and Coast Guard would be all over them, sound travels enormous distance under water and I'm sure that nothing is done to try and attenuate the noise coming from them. These things have no pressure hull so submerging the boat even sligthly would certainly be catastrophic.