The game doesn't check for them so it's your choice, but it's recommend to roll the PID and EC once because having two pokémon with those values equal to each other will look fishy, and you know, it's possible to extract replay data and look at it. Also if two pokémon have the same EC/PID and the same model (e. g. clones), if you put put them side by side on your box and hover the cursor between them, even if they have different stats their animation just continue running as if it was the same pokémon.
Basically you're just making them "a bit more legal and unique". Never hurts to do.
Also the PID isn't really tied to anything anymore and is only a legacy value used to determine shininess, so you don't really have to mind.