I fish out of a 94' Tracker tx17. It's got the flat deck as would any bass boat. I have owned a boat before that had the sunken deck, I didn't like it at all. I like to be mobile on the deck and move around if I need to reach out to fish a certain stump or tree. I jig probably 95% of the year, and the bass style boat suits me well for that.
When I see the sunken deck, it make me think of a spider rigging boat.
Just my opinion.