Freeweights have SO many advantages over machines. But hypertrophy-wise, it's often said that there is only a slight difference. I disagree in the case of squats, deads, and bench (may be others). There is just something besides the synergistic musclulature working that grabbing a weight and moving it with the body does that machines will never do, including real-world function.
Putting a box up on a shelf is better assisted by overhead presses, not smiths, you see? You need a LOT more going on besides tri's and delts.