I know what you mean. Thai groceries in the Alexandria area would commonly sell cilantro with the roots intact. But now it's rare that I ever see the roots. I don't think you'll ever see it separated from the cilantro tops.
My local Safeway (Columbia Rd) has had cilantro complete with roots a couple times.
Of all the Asian groceries around here, Duangrat's grocery consistently has the cilantro roots available with their cilantro.. though I haven't seen one recently. You might want to call and ask in advance when they will have one before making the trip. And when you find some, please do stock up! Chop off the roots and zipbag it in the freezer :) That's how I always have one on hand.
alkapa - I'd say different flavor; it's used a lot in Thai cuisine most commonly in combination with garlic and black pepper.