I would assume, too, that after all the present-day Collins family had gone through, and with Barnabas having been a close member for several years by series end, that Roger and Elizabeth would have protected Barnabas. It always bothered me when I read something, I think it might have been Sam Hall's article for TV Guide on "what happened" after the show ended, to the effect that "Roger discovers Barnabas' secret and tries to kill him." To me, that doesn't ring true. (But then Barnabas and Julia going off to the Orient had to be tongue in cheek, didn't it?)
I love the ambiguity the series left us with regarding whether or not Professor Stokes guessed Barnabas' secret. In my view, leaving things up to the viewer/reader to resolve, hash over, discuss endlessly, is a sign of respect for the reader's/viewer's intelligence, rather than spoon feeding us with all the answers.
(Not surprising that I find movies like "Memento" and "Gosford Park" brilliant ... )