I think the great hole in the plot is that the Jedi couldn't figure out where the ships were coming from. Did they only just notice that big mound that would most likely thrum with ancient dark power when Bastila told them about the dream? Isn't there some enormous space station that holds the Correlian system in an odd orbit? There was an amateur archaeologist, Cassus Sandrel, I wonder how long it took him to figure out what little he did. So the greater plot hole is that the Jedi couldn't figure out the existence of the Builders and the Starforge. Which is another reason why Malak bombed Dantooine.
Since Dantooine and other worlds are the Republic's bread baskets, then it's logical that merchants visit, Who did history? Trade is the most common way for knowledge to spread. Cerka knew about the enclave because they sold them faulty droids. Oh, my, people, work for, companies.
Dantooine was part of the Republic, Revan and Malak's corrupted followers (the non force sensitives) were from the Republic, the Sith were once Jedi. Many farmers of Dantooine joined the Republic forces, some of them might have become Sith also.
A "derr" is in order....
Sarcasm/]