No, not for a while. As I understand it they didn't have one at first but after some asshole used it as a backup (since they let anyone upload "music") and made a blog post about it they added one. Quite possibly they wanted to anyway and it was just a convenient excuse.
Thanks for asking, because it turns out I was wrong :(. I should know better than to rely on my memory these days. If you download the same FLAC file twice it won't be the same (possibly unless the two downloads are within a few days) but I just checked and they do decode to the same WAV. I haven't checked multiple accounts but when trying to find the article I thought I remembered I found someone saying they had checked and found them to be the same (not that long ago). I'm not sure if the FLAC or other specific file downloads are ever exactly the same between accounts, possibly not and they record the generation timestamp or such, but it seems the audio itself is not watermarked.
