Can having many files in a folder affect performances?

I've got an application that's going to generate about 20,000 files. To keep it simple, I'm thinking about putting all these files in the same folder. Am I likely to run into some performance issues doing so? My software is for Windows XP, Vista, 开发者_Python百科Seven and Mac OS X.

Any idea?

I know that Doxygen has a feature to break the generated files up into multiple directories because of slowness in access files in large directories under Windows. I don't know if this is just FAT or NTFS or both.