ext3 without dir_index has a limit of 32K directories in any one directory.
Where I saw it crop up was 32K folders under /tmp on a cluster system. So no it's not a limit on number of directories entirely (that's inodes), but rather how many subdirectories you can have.
ext3/4 has really poor large-directory performance, even with dir_index, especially if you are constantly removing and readding nodes. I would highly recommend XFS for large-directory use cases.
I got bit by this once, i think it was related to a maximum of 32k hardlinks per inode, which effectively sets a limit of 32k subdirs since each subdir has a hardlink to ".."
