Listen, this is coming from a Roy's perspective. Your pk fire and your upair juggles are absolutely essential to winning this match up.
Pk fire, because pk fire is EXTREMELY annoying for Roy to deal with. The only ways for him to avoid it are to DD around it, shield it, or jump over it, two of which take away lots of his offensive momentum. After that you should see if If you can hit him with pk fire in neutral, because you can get a grab for free unless they sdi it fast. Another thing you need in this match up is a solid punish game. That's where the upairs come in. Roy, being a fastfaller(think foxish fall speed), gets eaten alive by Ness's upair strings. After you tack on enough damage with juggles/pk fires/grabs out of pk fire, then you can backthrow Roy into the shadow realm because Roy's recovery is garbage. Also Since Roy relies on flare blade (his side b) to recover, you can probably pk thunder him for free but idk you have to test that on your own.