I think people are overestimating how well the submarine tracking works, and underestimating how noisy the marine environment is. I suspect that modern ASW only works in a moderate radius around the fleet it's supposed to be protecting, and that if you have a sonar sweep of every noise in the Mediterranean and subtract the ones with transponders, that's still hundreds or even thousands of small boats.

Even the surface refugee traffic overwhelms the limited naval intercept capabilities of the Mediterranean navies.