Wow! I never realised that the USS Enterprise (CVN 65) had disappeared off the face of the Earth for 9 months, while it visited another dimension, and then reappeared again. Yes, no one at all would have written endlessly about that conspiracy theory, and linked it to the man on the grassy knoll, and the faked Apollo 11 Moon Landings....although you might find some obscure reference book depicting the crew of the aircraft carrier USS Enterprise (CVN 65), it's highly unlikely to include references to their families, nor any classified data...
Maybe, if you don't mean a link between the research. The Pegasus experiments were with a Federation Cloaking Device, and I saw a clear parallel there to the conspiracy theories around WWII Radar experiments and supposed accidental access to other dimensions (IMHO all rubbish) which were the basis for the film The Philadelphia Experiment and The Philadelphia Experiment II. I agree though, those Pegasus events (if not the Philadelphia events too) were expunged from the history of the future, so why not Spore Drive too.That (above) said, I can't help but see a parallel in the spore drive and what the Starfleet ship Pegasus was trying to do.