“Trevor Lawrence is all but assured to be the No. 1 pick by the Jacksonville Jaguars, and most draft experts believe BYU's Zach Wilson will go No. 2 overall to the New York Jets. That leaves Ohio State's Justin Fields, North Dakota State's Trey Lance and Alabama's Mac Jones as the three QBs expected to be available at No. 3.”
Then you have the betting lines:
This had Zach Wilson has the heavy favorite to go 2nd overall as of March 10, two weeks before the 49ers trade. At the time of the draft, Wilson was -5000 to go second overall.
If 100% certain means the Jets had already made the pick, then no, the 49ers didn’t know the Jets were taking Wilson. But anything less than that, yes, the 49ers knew Wilson was gone at 2.