I'd also say the Sox do draft pitchers, roughly just as many pitchers as position players. The thing is they usually don't draft pitchers with their first couple picks, and the few times they have the last decade they've gone bust (Groome, Ball). I feel the Sox inability to develop homegrown starting pitching is truly a combination of factors.
1. their bias towards up-the-middle position players early on in the draft
2. Their ability to scout, draft, and develop arms.
3. Luck, I think luck plays a large role in it because developing pitching is really really hard and effectively you're trying to predict a human being's future. Which is also hard.
Can't do anything about #3 but 1-2 you can. And as you said, it takes 3-4 years to even notice those changes. For all we know they've made changes and have a great system in place now.