Isso foi discutido na lista freebsd-questions em novembro de 2008. Para citar Erik Trulsson :
Each i-node on the disk contains a field telling how many hard-links point to that inode. This field is a (signed) 16-bit value, meaning the maximum number of hardlinks allowed is 32767. Each subdirectory created contains a hardlink ('..') to its parent, thus limiting the number of subdirectories to a single directory to less than 32767.
Note that this does not limit the number of files you can have in a single directory, since normal files do not contain hardlinks to the parent directory, but there are of course limits to the total number of files and directories you can have on a single filesystem based on how many inodes were created when the filesystem was first created.
( Mensagem completa , start of thread )
Estes são limites teóricos; como discutido acima, você começará a ter problemas de desempenho bem antes de atingir qualquer limite.