Having big legs will not make you throw harder. Squats and deads will make your core quite a bit stronger, though, which will make you throw harder if you have proper mechanics.
It is important as a pitcher, though, to have good endurance strength in your legs, because your delivery is easily affected when they become tired. So definitely do the leg work, just understand that you don't need huge legs to throw hard.
Of all the pitchers I played against in high school who were drafted or went D1, I would say that 75% of them were tall and lanky.
If you want to throw harder, play a lot of long toss (back off when your arm gets sore), throw a football, and stretch your forearm and shoulder.