From what I have read the general consensus is that if you use a fast draining soil mix, it will drain. Putting stones or bark chips in the bottom of the pot just decreases the useable volume of your pot. I know some people still do this, it wont hurt your trees.
There is another scenario here though. Sometimes people have trouble with their pots blowing over, adding stones to the bottom can add more weight to resist the wind. The catch is your adding more weight to move around in spring and fall.