no, Nikki and Paulo were not part of the show during seasons 1 and 2. They were added to the cast as part of season 3, and then inserted into the storyline, as if they've always been there. So the footage of them being in these scenes we've seen before has either been digitally manipulated to have them added, or been re-filmed to have them in it. I believe a little of both happened, because I doubt they'd re-film the whole crash scene again, but some of the scenes were obviously newly filmed, like when they interact with Kate talking about the key for the gun case, for example. (and parts of the crash scene were new, like interacting with a pen-searching-Boone)