Well to be fair, neither species names were mentioned in those episodes of Enterprise. A cop out, I know. So the starfleet databases would only have mention of a cybernetic species, and a capitalistic one with big ears.If this is common, it would explain lack of knowledge of the Borg and the Ferengi (and how much else?).
So after first visual contact with the Ferengi in TNG, someone at starfleet who knows of archer’s adventures might recognize them and go ‘oh shit’.
As for the borg, the Hansen’s were investigating them before TNG. They had a database page Stardated to pre-TNG (technically I think the stardate was from Undiscovered country)