I've never gotten all 100 before. I usually end up with 55-65 because if I see or hear a Gold Skulltula, then I'll pursue it, but I don't persue the ones in the most ridiculous of areas, and I DEFINITELY don't do the ones that involve soft soil patches. (Emptying all your bottles for Spiders, then hunting down soft soils hidden remotely across Hyrule, just for one Gold Skulltula doesn't seem worth it to me)
As long as I get all the rewards from it (excluding the Final Reward, which isn't all that worth it, because by the time you have 100 Gold Skulltulas, you totally need 200 Rupees, amirite?) I'm fine. Luckily, I can go through the game getting Skulltulas as I please and still end up with 55-65.