If I recall correctly, I think this is usually explained as a thermocline effect where as deeper water gets churned up and mixed in the wake, it is a different

If I recall correctly, I think this is usually explained as a thermocline effect where as deeper water gets churned up and mixed in the wake, it is a different temperature than the surrounding water outside the wake. This water has ever-so-slightly different fluid characteristics and so it presents a bit of a barrier to the usual diffusion and mixing you might expect. There's also the potential for a very thin layer of some type of hydrophobic substance (like an oil) to be left behind that can dramatically reduce waves in that area. There's youtube videos around for that effect.