It really doesn't matter. A 2-way deal just means that he would make a different salary with the Marlies than with the Leafs. It has nothing to do with waiver eligibility. And since I'm pretty sure that Smith will be making under $925,00, it has no cap implications (only a player's AHL salary in excess of $925,000 counts against the cap).
Trevor Smith's contract is for $550k (league minimum).
We knew going into the summer that Leafs had cap issues and would need to find a bunch of players making <$1.5 mil to fill out the roster.
With the Smith signing Leafs now have 18 players under contract for next season with (Franson, Gardiner and Reimer still unsigned RFA's).
However at that price it would allow young Marlie forwards like Holland, Ashton etc to beat him out for a NHL job and Smith can go back to captaining the Marlies as he did last season.