The difference between 98% and 100% is borderline zero. It may even be literally zero; I mean there's a chance it doesn't EVER make a difference in your whole gameplay time from now till you drop the game. It's more about collector value imo, in which case it doesn't matter if you catch a perfect one in 2 weeks and never power it up. It's still extremely rare.
That said, it's the best electric pokemon available so you want to power it up. If you have decent electric attackers (powered up Jolteon or Ampharos) and can't spare the resources right now you could focus on Scizor (to prepare for Mewtwo) and delay powering up Zapdos.