Yes. Seriously.
As I indicated in my comment the way to determine what directory hierarchy will be "fastest" is to perform performance tests on various configurations, and select the optimal one.
The canonical capacity planning question has information on how to do such benchmarking (and we generally assume our users are smart enough to make changes based on those results).
The difference in specificity is why I left a comment on the question suggesting they investigate the cause of the poor performance more thoroughly - this could be expanded into a longer answer if we knew where the bottleneck was, but without benchmarks and a better idea of what's causing the slowdown I think it's pretty tough to give useful advice beyond "Run some benchmarks".
That said, if you can make a sound case for why Gibson's question is different enough that it is not a duplicate (such that it convinces either one of the moderators or 5 voting users that the question should be reopened) please do so - If you can give a better answer to this question than the generic "go benchmark" I've got no problem reopening it.