The original Bronze Age Boat is unlikely to have sunk through hazard, as it was insider the port, in a side-stream of the Dour. Even if it had gone down in bad weather, they'd have had no problem retrieving it there and then.
It may have been left to sink after some useful parts were taken from it, possibly as a decommissioned vessel. This may be one of the reasons why the boat does not seem intact - the other reason being that one part is still buried in Bench/Townwall St.
I hope they are careful to explore the DTIZ area before building on it. There could be quite some ancient artefacts beneath the surface.