The only downside I can think of to recessed coamings is that they're more complicated to build. Other than that, it's all upside. I don't think I've ever been in a boat and thought "I wish I had a higher coaming on this thing." Lower is better.

That said, the recess has to be properly sized to allow the easy installation of a spray skirt with gloved hands. A poorly designed recess can be a serious liability.