Things like the Internet Archive have an opt-out process rather than opt-in. The extent to how the IA operates within the law isn't clear to me, but it does suggest that the case isn't as open-and-shut as you make it seem.
Internet Archive operates the same way, if they receive DMCA notice, they need to comply in order to keep the safe harbour process.
As to whether WTL will file a DMCA to take down his material, it looks unlikely. For whatever reason he suddenly wanted to be out of limelight and I get the feeling that he doesn't care much whether his work is shared or not but who knows, maybe he will come out of the woodwork to raise his voice (which would be in contrast to his reclusive state).
He really is a mysterious figure and even more mysterious is the sheer amount of effort he put into his work and passion to share it suddenly relinquished overnight, out of whim? stress? depression? We can only guess.
They have removed web sites before due to copyright claims and have a DMCA claim process.