I wonder would the proposed harbor locations have left any structure to indicate that they were in fact harbor temples rather than just temples?
I also wonder how much the river moves within that flood plain. I lived in a flood plain at one point and the river even season to season seemed to "move" a noticeable amount.
At Wadi al-Jarf[1], one of the oldest harbors in the world (~2600 BCE), they discovered numerous stone anchors, a stone jetty, and storage galleries carved into limestone that contained several boats, sail fragments, oars, and rope. They also found jars that have been discovered at another site across the Red Sea, indicating they may have been used for trade.
I would expect that harbors were mostly made of wood. Stone is too heavy and would sink into the bottom, and they didn't have access to enough metals to think about bronze (much less iron). Wood of course rots - while the climate in Egypt is the most conductive to wood not rotting, if it was a harbor structure I'd expect (read I'm not sure here!) that the area remained as a swamp for a while thus rotting away anything left behind before to fully dried up.
Ancient Egypt was notoriously wood-poor. Stonemasonry was developed to a high art there (in both senses of the word) out of necessity.
Many Egyptian watercraft were made not of wood but of papyrus. Where wood was utilised, it was imported from elsewhere (Lebanon, famous for its cedars, and acacia, possibly domestic in origin).
Amongst Egyptian relics, wood stands out as a high-value material reflecting its scarcity and imported status.
Other possible shipbuilding materials, not likely to have been available or widely used, would include animal skins (as with Inuit kyaks), water-proofed cloth (unlikely, though cotton was abundant), metals (unlikely), and concrete (again, highly unlikely).
Papyrus has even poorer survival characteristics as a shipbuilding material than wood, though some relics are extant.
The oldest surviving dugout canoe found could be as old as 10k years old. Certainly a number of ancient Egyptian boats have been found and dated to around the time of the pyramids. So dock piles could possibly have survived.
Of course there were no doubt a large number of boats and only a small number of temple docks.
Egypt's deserts are about the perfect climate for preserving wood. However the area near water is not desert and so not perfect. Boats would be moved, but the piers (such as they were in those days, I doubt we are talking a modern shipyard structure) would remain in the water, and in general when a river moves the area remains a swamp long enough for any wood to rot.
The type of wood used maters, some wood rots much faster than others. Boats would have been made from rot resistant wood since they are in the water. I wouldn't be surprised if they used any old wood for the piers since the water course and floods mean the piers need to be rebuilt every year anyway - but this is pure speculation.
I also wonder how much the river moves within that flood plain. I lived in a flood plain at one point and the river even season to season seemed to "move" a noticeable amount.