I am painting my jon boat and need to remove the doors of the storage and live well.  They are curretly riveted in and would (I imagine) need to be reattched with rivets to close flush.  Has anyone done this before and is it difficult?

I was told by a buddy that you have to drill them out and that will be the most difficult part but I have to be careul with the bit I use as to not go too large. As far as reattching rivets, I have a rivet gun and have the correct sizes but it seems like I just pull the trigger on the rivet gun.

Any other things or tricks I should know?

Your buddy is right.  Just carefully drill them out and put new ones in their places when you are finished painting.

Most of the time the originals are beat down and not pop type for a reason, if yours are so be it. If you want better quality hardware and maybe the better original type beat down rivets, go to a commercial place where they will have such things. They will have signs that say to trade only and not public. That is because so many give bad checks and credit cards, take cash and be ready for what you need so as not to waste their time and they will not only give you better stuff, but at an even lower price. I can get a dozen drill bits at the one I go to for the price of 2 at home depot. There are also on line shops that are similar selling more varied and better stuff than HD or lowes, I have no reason to ever return to HD or lowes. Stainless and aluminum come in different grades, HD and Lowes offer bottom feeder quality stuff and dont even kiss you when they are done.

example but there are many

http://www.hansonrivet.com/

http://www.rapidrivet.com/

I know Lowe's and HD sell junk but what kind of rivet do I need?  The only rivets I see everywher look like little swords and I don'tseehow they will hold the door to the hinge.  

Is there a double ended rivet?