[Experience with ISP-class mail spool management elided]
There are definitely performance issues with super-giant directories, but I don't think of 1K or even 10K as super giant. On the other hand,
[...]
It has been my experience that dealing with large directories (for values of large in the range of 10^5-7 files) that the most cost effective performance optimization technique is to re-engineer the software in question to use another method. Splitting into different directories is usually the solution. For mail, using a subdirectory of $HOME as netcom did, or for file caches, in my case, doing progressive /[0-9]/[0-9]/[0-9]/whatever trees worked for a while. We eventually moved to Oracle. While Oracle isn't fast, it at least has a predictable, and very gradual, degradation curve.
-j