According to their menu on wdwinfo.com their hours are 11:30 - 9:00pm, with hours varying during special events. I would assume the Super Bowl would be a special event, so my advice is to call them directly to find out more. However I can't help you with the other question you have since I have never been to WDW during the Super Bowl.
However I have been to the Boardwalk before during the BCS National Championship Game back in January 1999, expect at the time I forgot the game was even happening because I had wanted to try the ESPN Club, so it was a total fluke we went the night of the game. Anyway when my family and I got there the line was way out the door so we left right away and this was 2 hours prior to kick off. So I would guess it might be the same thing at the All Star Cafe.