If there's a hidden pool of FBDD talent, it is most likely in industry, not in academia. Fragment-based approaches are occasionally mentioned in courses or lectures by professors who want to appear up-to-date. But the only folks actually doing fragment-based work (as distinct from structure-based methods) are in a few key labs, all led by PIs with prior industry experience.
If you look at the 2008 FBLD Conference poster session, almost half of the presenters were from a single academic lab. The rest were largely virtual docking, traditional medicinal chemistry, or people from industry. One of the conference organizers told me that there were less than a handful of us graduate students in attendance; compare that to attendees at any given Gordon Conference. So I believe there are "puddles" of FBDD here and there, but not what I would call a vast resource.
That said, it seems the skills one needs to do FBDD can be acquired by other means in academia (ie. structural biology PhD, synthetic chemistry training, etc.). But if companies are looking to hire PhDs well-versed in fragment-based methodologies, there is currently not a huge group being freshly minted each year at commencement.[Ed Note: I also think it is interesting that the industrial types that go to industry fair not well in terms of grants and such (my impression talking to the ones I know). But, I would be interested in hearing from those types also.]