I'm bothered by the idea of a strict limit. Instead, I think it's exponentially more difficult earlier in time. So maybe 12,000 works sometimes. If really pushed, maybe 15,000. But 100,000 is almost certainly ridiculous.
[Edit: I also think methods for looking earlier should not be eyeballing dictionaries. They should involve systematic reconstruction and use of the earliest records then comparing those to each other. It will never go anywhere to compare what languages look like today to what they might have looked like a long time ago, without serious/rigorous backtracking. It is still likely to fail at a certain time depth, but if anything that's the right method.]
Also, I meant to add above that the Khoisan group has been questioned recently and I have a few references to that effect if you're interested:
Güldemann, Tom & Edward D Elderkin. 2010. On external genealogical relationships of the Khoe family. In Matthias Brenzinger & Christa König (eds.), Khoisan Languages and Linguistics: Proceedings of the 1st International Symposium January 4-8, 2003, 15–52. Köln: Rüdiger Köppe Verlag.
Heine, Bernd & Henry Honken. 2010. The Kx’a Family. A New Khoisan Genealogy. Journal of Asian and African Studies 79. 5–36.