Paul Farace probably can best answer our questions as to when and why the Bowfin folks poured concrete in the bow and stern.
There's no question that a museum submarine still in the water needs a little extra ballast. If they sit too high, they could be prone to rolling over.That's why the Navy either put concrete blocks or poured cement (according to John D. Alden's "The Fleet Submarine In The U.S. Navy") in the empty battery wells of mothballed boats when they were prepared for Naval Reserve trainer duty.
But I don't think IMHO that putting cement in those bow and stern areas would be that much of a help. The battery wells would have been much closer to the center of gravity and provided the necessary stability. And cement blocks would have been much better and not retained corrosion-producing moisture than poured cement.
It seems that the Bowfin folks run a good operation and I imagine that it would have cost more money to restore the bow and stern tubes with shutters, money that, as we well know, is not always plentiful at museum submarines, sorry to say.