There don't need to be any conspiracies to suppress information about the Borg for the Federation to have been unable to put all the data points they had together by 2365. You're talking about trying to connect the dots in a Federation that is amassing unquantifiably large amounts of data about the galaxy for the better part of 200 years.
I mean, hell, agencies of the U.S. government were aware of the potential threat al-Qaeda posed in the years leading up to 2001, but the U.S. still wasn't able to put the pieces together in time to stop 9/11.