I believe I was told (2-3 years ago) by an employee of the Nekton that they used to do the Blue Hole but it turned out the guests weren't that interested. They found that most guests had done it already and would rather do 2 dives at another site than the 1 dive at the BH. So that is why they dropped it from the itinerary.... don't know if it's true, but I can see it.
Also, since the Nekton does Cay Sal Bank in the Bahamas - anyone wanting to do Blue Holes and see really cool stuff, should do that! We loved it.... we did 5 different Holes and they were very different in size and topography, some covered with life and some just big holes with sharks darting in and out. A few even had long swim-thrus from +90' depth up to surface! I would highly recommend this trip to anyone looking to experience Blue Holes. It is a great trip with 3 FULL days of diving Blue Holes and the other 2.5 days doing other reefs.
robin