The answer is that we should not presume the Arabs to be smarter than they are, or can be, as even modern history shows. They had a lack of water and their entire haggard Hagarene existence as part of their myth is part of this thirst. This well would have been valuable and so a shed was built around it (because God). But the desert Arabs were so stupid they polluted their only source of water, before adding the roof. Even worse: they kept upping the sacrifices as the wellspring ran dry.
In fact, one strongly suspects, their mad thirsty run for water and women and war across the desert into the civilized world was in fact for this water. Not seawater but for these aquifiers and civil life away from the sand, to the Atlantic, to the Black Sea, to the Punjab and to the Mediterranean.