Assuming YouTube does dedup on their backend then this is the same issue that megaupload has to deal with before they were taken offline. Namely, if an infringing file has multiple links pointing to it, is the platform obliged to take down all of them when presented with a DMCA notice? If so, is the platform then obliged to take down every slightly different version of the same infringing content? Where do their duties end?

As much as we malign content it is still more workable than having YouTube manually purging all videos that appears to be infringing based on very little information. And most content creators who sample copyrighted media under fair use have learned to cope. The more egregious issues are more concentrated around misattributed licenses and musical performance.