There's not really a good spot on the nose where you can say, "There's the docking port!" Add it to all the other things that weren't really defined (or changed later) on the Defiant. Size, tractor emitters, the shuttle bay, armament, docking ports...they were all seemingly kind of made up as they went along.
Does it really matter, though? I can't really blame them for not putting a lot of thought into something that's so irrelevant to the plot.
But then again I never cared for Trek ship blueprints much either. Voodoo science doesn't really appeal to me.