I agree that it's misleading. Saying that 99.9% of species that ever lived are now extinct, if we're including species that are ancestral to now existent species, basically all that's being said is, "Most of the organisms that have ever lived are dead."
Well, obviously.
Nothing stops evolving, so given a few million years, more or less, (and much less for organisms with faster reproductive times) you're almost certain to have a new species, if for no other reason than genetic drift. If that's all that's being said, it's not really very interesting. At least not in the context of Hitchen's remarks.
On the other hand, what percentage of species that have ever lived are not now existent or ancestral to one or more now existent species? Probably a much more difficult question to answer.
I wonder if the answer is very much different, however.
I think basically the problem that I have with the statement is that when you talk about extinct species, must of us think of species going extinct. That didn't necessarily happen to homo erectus. If there's a continuous line of decent, then a species can be extinct without an extinction event.
And personally, it's only such extinction events that seem to have bearing on the point that Hitchens was making. Or that most people make when they bring up the "99.9% extinct" figure.
Mind you, I think his point still stands, even if the figure for the value that I think is important is much smaller.