The problem they found at Duxford was that the watertable was too high [the hole would be very deep!]. I think Duxford was on the list because it was an active RAF station. The silo would not have taken up that much space, and rather than requisition land, I think they thought it easier to use existing MoD land - and preferably an RAF station, as the silo would have manned by RAF personnel.
However, I think a lot of it was still up in the air at the time of cancellation. Although the cancellation was not announced until April 1960, the silo concept was dead by December 1959.
Nicholas