I had real experience with about 100 000 files (each several MBs) on NTFS in a directory while copying one online library.
It takes about 15 minutes to open the directory with Explorer or 7-zip.
Writing site copy with winhttrack will always get stuck after some time. It dealt also with directory, containing about 1 000 000 files. I think the worst thing is that the MFT can only by traversed sequentially.
Opening the same under ext2fsd on ext3 gave almost the same timing.Probably moving to reiserfs (not reiser4fs) can help.
Trying to avoid this situation is probably the best.
For your own programs using blobs w/o any fs could be beneficial.That's the way Facebook does for storing photos.