It hasn’t been that long (30 years???) that the archaeologists put that together with regard to the rising ocean levels, and have shifted their search to offshore.
Or perhaps they figured it out awhile ago, but now have cheaper ways of exploring the ocean floors.
A bit of both. It used to be ignored or wasn't considered, then was done obliquely (the Cosquer Cave in France, the entrance has been underwater since the glaciers went), and now, the technology has become both better (unmanned, they can go deeper, and there's no problem with shortened stays the deeper it goes, as with a human diver) and cheaper.