The links you get to that "folder" will not benefit any other pages within that folder (well directly anyway).
That's rather an odd statement. The value of inbound links flows from the target page to other internal pages linked to from that target page. Given that the index of any folder is more likely to point down to other pages within that folder those other pages are going to benefit more from those inbound links than other subpages on the site.
If you get links to
www.mypage.com/folder/ or
www.mypage.com/folder/index.html it makes no difference, its still treated as the same page.
Not quite. Google has started to identify / and /index.ext as one and the same, but this has only really come into effect in the past 4-6 months. Best bet here is to use one or the other URI convention throughout the site, and if possible set up 301 from /Index.ext to / or vice-versa.
Make sure when you decide how you want to setup the site structure which one of the above links you want to use and only link to one of the with your internal site links. Otherwise you link equity will be shared between the two domains above and they will both have the same content.
http://www.mypage.com/folder/index.html
Shared between the 2 URLs perhaps? Google handles this pretty well now.
Key to this is probably going to be getting the right anchors pointed at your deep content. Of increasing importance of late is where those inbound links come from - geo-targeted results coming more and more into the fray these days.
Rgds
Richard