It's not just ntfs. I tested this a few months ago in a pretty unscientific manner using ~50 million files in one directory.

btrfs was unusable (not only that particular directory, but the whole filesystem became noticeably slower).

ext4 was ok. xfs didn't break a sweat. I don't recall any practical difference when compared against a nested tree like

  ├── aa
  │   ├── aa
  │   │   └── aaaaf3ee5e6b4b0d3255bfef95601890afd80709
  │   ├── ab
  │   └── ac
  └── ab
      ├── aa
      ├── ab
      └── ac