1000 files seems pretty low as a default. Looks like it might be a bit out of date:
INT_SETTING(F_BANFROMQS, max_files_in_dir, LANG_MAX_FILES_IN_DIR,
#if MEMORYSIZE > 1
1000,
#else
200,
#endif
"max files in dir", UNIT_INT, 50, 10000, 50,
NULL, NULL, NULL),
Only a handful of low-RAM targets have 2 MB -- everything else is >8 MB, so I'd argue the default limit should be upped quite a bit.
And I don't think there's a problem with increasing the max limit beyond 10,000.