Hi Joe,
The search results only displays content that is in the search index. ModuleWrapper is just a container for other content there is nothing I can do to make it write to the search index, it would depend on the internal feature hosted in it to index its content, but even then it could only go into the search index if it were directly on a page otherwise the search index doesn't know how to link to it. Any content instance loaded inside of a ModuleWrapper has no idea it is inside one and has no idea what pages if any the modulewrapper is used on. Considering it is used in layout.master then the even if the search engine somehow knew about it then I guess it would have to list every page in the site that uses that skin in the search results. Its not feasible. Even so, content that is on every page is easy to find so one should not need to search for it.
I can say that for the next release we will have the option to use google or bing for site search instead of or in addition to the internal site search. Since those search engines are crawling the pages they would see any content on a page including content that is loaded from a ModuleWrapper. Those search engines may do a better job than the internal one for some things, but they can only crawl pages with no role security applied, whereas the internal search can find things on protected pages and only show the protected content in search results to users in the roles allowed. Of course google and bing will only work as site search once the sitemap has been submitted and they have crawled the site, it won't work instantly for new sites.
Best,
Joe