YouTube will use the same basic defense that police organizations use in relation to seizing proceeds of crime. You don't get to make earnings on legitimate stuff through the use of illegitimate stuff. Whether it is mentioned in the terms or not explicitly is irrelevant.
If you upload significant copyrighted material (enough to get shut down for), then your earnings for any legitimate content are often held back by YouTube. The logic is simple. You used the copyrighted content as a method for generating views on other content on your channel. Thus, you are not entitled to that revenue either. It is very unlikely that any sympathy is to be had here.
To take that a step further, it is often the case that channels will upload copyrighted content in order to build a viewerbase first, deleting the copyright offending content later assuming they didn't get shut down by that point. They now have a viewerbase and didn't do any of the work needed to get it legitimately.
It's YouTube saying that they know you uploaded copyright material intentionally, and that you don't deserve to earn any money on their site. Don't act surprised.