Idaho was moving around in stolen ornithopter (one mentioned in Baron's and Piter's conversation in the presence of Duke Leto), so Harkonnens had pretty good idea who could that be ("Halleck, Hawat. Possibly Idaho."). And when he went to fetch Kynes - which was his second flight - on the way back they were attacked by Harkonnens. Since attack was defeated using decoy and big shield, the result was noticeable:
"That blast will attract considerable attention, Sire," Idaho said.
So Harkonnens had approximate location for search of something and if there was any report that it was that stolen 'thopter, they made sure to be thorough.
And then there's this:
A Fremen emerged from the hidden area of the chamber, spoke to Kynes: "Liet,
the field-generator equipment is not working. I am unable to mask us from
I think the three facts: stolen 'thopter, that it was done by someone highly skilled and someone operated in the desert with working shield basically screams what is going on. Not sure if Piter was still alive at that time, but there is no need for a mentat to figure that one out, anyway.
As to your more specific question (the one referencing Baron's (..)lead to them(...), I think it needs to be interpreted in broad context of search for Jessica and Paul after it was discovered they slipped Harkonnen's grip, and NOT in specific context of some scheme. Baron is not beneath or above making any of his statements seemingly based on his own predictions, so it may equally well be an image-related, and not performance-related (if one can call it such).