The Mets declined to offer arbitration to Steve Trachsel and Cliff Floyd, neither of which figured into their 2007 plans. Floyd has drawn interest in several American League teams looking to play him primarily as a designated hitter. Trachsel can take a short walk off a long pier.
There's not much risk in offering arbitration to Mota and Hernandez. I think the Mets have genuine interested in resigning Mota, even though he won't be available until midway through May. Neither pitcher would cost a lot in arbitration (side note: it would be interesting to see if and how the PED rap would affect Mota's arbitration leverage. Further, one has to suspect that the fact that he'd only be eligible for 112 of the team's games if that would further impede his bargaining power), and both are still serviceable-to-good relievers.
I think the ideal situation would be for Hernandez to sign elsewhere, allowing the Mets to cash in on those draft picks for an otherwise average relief pitcher, and to resign Mota with the hope that he will keep himself in shape and be ready to go at the end of May.
UPDATE [2:42pm]: Hernandez has signed a one-year deal with the Indians, so that means a couple more draft picks are coming the Mets' way.