Omeka S 2.0 didn’t make any changes to PDF thumbnailing.
Probably you got an updated ImageMagick on your server that disables PDF reading. See for example this post about an ImageMagick policy file some distributions have used to disable PDF support by default.
As I noted in that thread, the distributions put those policies in for security reasons due to an exploit: at a minimum make sure, if you’re going to re-enable PDF support, that you have an up-to-date version of Ghostscript.