I'm wondering if I would actually put any structure directly under the dock as it could impact fish through that cut-out hole in the dock floor.

Layering structure all around the dock (but excluding the deep/open water side like Scott said) seems like a winner.

Excerpt from Robert Crais' "The Monkey's Raincoat:"
"She took another microscopic bite of her sandwich, then pushed it away. Maybe she absorbed nutrients from her surroundings."