Perhaps a causeway above the water would take a much greater battering from the sea. Build something lower and it may last longer.
Tidal Venus pools must work because of the tide. Rather like a dry dock. Float in on the tide, close the gates and expel the water if necessary. Presumably the Venus pools would have to rely on the ability to float in on a high tide and remain there once the tide had dropped, unless I've got the wrong end of the stick.
The Mediterranean doesn't have tides in the oceanic sense but it was much lower in the past. We know that by the flooding of the Black Sea and also with the finds off the coast of Spain, Egypt and elsewhere. Large areas were flooded.
Cyprus has an importance if we accept that it was the main source of copper. The north eastern arm seems to point directly towards that huge oblong 'dock' type area in the corner as the land does a right angle south. On the google satellite photographs we can see long piers with ships tied up. If it's perfect harbour today I would imagine it would have served the same purpose thousands of years ago. With the lower level of the Med I would imagine that north eastern extension to Cyprus would have got very close to the mainland and provided every opportunity for a causeway.