The problem with this note is that one doesn't know just what Hoover knew (or didn't know, or thought he knew, etc) when he wrote it.
Looking at the note itself (
http://articles.dubroom.org/hoover_ufo_memo_big.jpg) it seems perfectly reasonable to assume that Hoover didn't need any knowledge whatsoever of any actual disks- simply that he wouldn't refer cases of UFO investigation to the army or air force unless they could promise him access to any future recovered disks. The La. disk cited Hoover had no access to, therefore, he couldn't know if it was real or fake.
Additionally, consider the history of J. Edgar Hoover and his FBI at the time. In 1947, Hoover and the Army were not on good terms, Hoover was furious that the OSS (with its roots in the Army under Bill Donavan) was being turned into the CIA and both had been given jurisdiction over foreign intelligence activities, something Hoover coveted. It is very reasonable to believe that the Army wouldn't tell Hoover much of anything unless forced to, be it about real disks or hoaxes.
Hoover, as well informed as he may have been, was not the most powerful man in America. He had a major blind spot- the rest of the federal government, which he antagonized and fought with incessantly, and which would not cooperate with him and with which he would not cooperate. (He was a survivor, though, managing to jump ship by abandoning his friend Senator McCarthy, just in time before the Army-McCarthy hearings.) This blindness would be his eventual downfall, by the Nixon era he was living, like all men of his leaning, in a virtual information vacuum.
As for J. Edgar Hoover the man (and this is just a hunch) it seems very hard to think of him as having a greater interest in flying disks than the general national zeitgeist of the era- which is to say, he may have believed them credible but not necessarily given them much more thought than being simply another irritating bone of jurisidictional contention between the FBI and the rest of the Federal government.
