It is my belief that autolinks would improve the ranking of your wiki pages compared to other pages in your site, since the wiki pages would be linked a lot more within the site thanks to autolinks. It would imply to Google that the wiki page is an important part of your site, since you link to it from a lot of other places on your site.
Autolinks would also help search engines crawl your site and find wiki pages that they might not find in other ways.
However, I don't believe that autolinks on their own would improve the overall rank of your web site as a whole, just that wiki pages would rank better compared to other pages in your same site than if you made the same comparison without autolinks.
On the other hand, I don't think the popups play much role in SEO, just in helping your visitors learn more about a topic or enticing them to visit your wiki. Since the popups are loaded on demand when hovering via Javascript, the related snippets would not ever be seen by most current search engine crawlers. However, whatever search engines (perhaps Google) track user interactions throughout a site might be able to give greater weight to the target wiki pages because they noticed your users who looked at the popups actually clicked to read more.