Yup, quite a bit has changed in the last few years. For example "Ultimate SEO URL" has been replaced with "Ultimate URLs" (and is very easy to install)... And CEON URIs has been updated and additional tools created to make CEON URIs easier to manage... If you are currently trying to test the latest versions of either and having difficulty, suggest posting in the respective Support Thread and providing all the relevant information and answering all of the questions asked.

Of course both of the above work best "out of box" when best practices are followed (templates all use zen_href_link, only one site per VirtualHost / web server document root, dedicated SSL certificate, Zen Cart patches kept up to date, etc).

Yes SEs are not inhibited by (or having issues accessing) URLs containing ? and & (been a very long time since this has been an issue). But SEs are all about providing a "human friendly" experience (in addition to being easy to parse programmatically). Modern SEs also show URLs in the search results.

So while one does not NEED alternative URLs, one may wish to use them to improve a website visitors experience (as well as the store owners experience - such as when looking through analytics).