Only the .jar files are "cleaned up". The .json and folder itself will still exist in the versions directory.
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The folders are cleaned up upon next startup of the launcher – probably a Windows thing that the launcher doesn't take into account, not unlike the natives only deleting after the launcher is closed.
Note: Sometimes it takes multiple startups to fully delete the folders.
Cannot confirm. Deleted my profile "14w17a", started Minecraft and the whole folder
./minecraft/versions/14w17awas zapped.