"Can anybody shed some light on how non-deburred condition affect fatigue life of a joint?" … umm, it destroys it !
plenty of aircraft accidents have been caused by damage initiated by a burr.
you're not, I hope, working on your own; so there should be a "typical practices" book around … your standard manufacturing processes, your standard engineering design practice.
FAA AC43-13 is not a bad place to start. I'm sure there's lots of stuff out there (like "repair design" engineering courses) that'll let you.
"good" places will size up a doubler, temporarily install with clecos, then full size the rivet holes, remove the doubler, deburr, install dblr with fay seal and clecos, and rivet away.
But there are also plenty of places that'll fit with clecos, remove dblr, install with fay seal and clecos, and then full size the holes and install rivets.
No one can say either procedure is Right or Wrong.
What sort of structure are you dealing with ? 'cause if it's secondary structure, then it's game on !
another day in paradise, or is paradise one day closer ?