I was not aware that ID ever recognized or converted text to hyperlinks. As far as I know, that's a function in whatever software is reading the output from ID.
Seems I've never noticed the Type > Hyperlinks and Cross-References > Convert URLs to Hyperlinks command. Is that what you are talking about? Apparently that's a behind the scenes GREP find/change query. You might want to look at what the query structure is here: http://forums.adobe.com/message/4619499 and write your own that includes the trailing slash, if it exists, and adds the protocol (though I think that might be a bit more of an issue).
I am running CS6 in Windows 7 on a 64-bit operating system. I'm converting URLs to Hyperlinks. My files consist of college information data. Here's an example of a URL that does NOT convert right: http://www.anystate.edu/a/business/department/computer-information-technology/. When I export to epub the hyperlink stops before the first hyphen. I get http://www.anystate.edu/a/business/department/computer and the rest is not hyperlinked. I also have URLs that won't convert if there is %20 or /~ in them. And I agree, all URLs should convert and insert http:// in front of them. I have to fix these manually. The only way I know how to speed this up is to "search" in the epub html files for the closing anchor code followed by a hyphen or slash and then cut and paste the text into both the hyperlink and the text. That's tedious! Any suggestions would be appreciated. I'm assuming that Adobe has done all they can do.