I will concur with the original observation that avoiding directories with too many entries is an excellent plan on *nix systems.
What constitutes "too many" is variable, but generally has to do with the filesystem's implementation of directory storage: if you get the directory contents into extended blocks, things will become unpleasant.
In general, if
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ls
takes more than a second or 3 to start returning results, your directory is too full, and you should hash it somehow.