That is extremely disappointing news. I have always preferred the readability of YUI to jQuery. Although server-side Javascript implementations like they suggest would be ideal and improve UI performance, it is not realistic to expect widespread server support for at least another few years, at least when you are developing software like VaultWiki, which has to consider a wide range of server setups. To be honest, I had not even heard of Node.JS before September 2013, and everything I read about it at that time suggested it was still very basic and in its infancy.
Even so, I have not encountered any bugs in YUI itself since early 2011, and have not really had a great reason to keep it up to date since that time, except to occasionally improve performance and to remove deprecated plugins that VaultWiki doesn't even use. So, I don't think this decision is so devastating that we need to immediately start considering other libraries. By the time we do need to, perhaps there will be more widespread server-side support and we can start using those kinds of libraries.