Minor correction; side missions don't count, at least in BotW. I have no idea (yet) whether this also applies to TotK as I haven't beaten the main boss yet and can not verify it myself, but I do have a full breakdown for Breath of th Wild ;)
I still don't really understand WHY Nintendo opted to make this counter so awkward and counter-intuitive in the first place tho. An actual, real, "overall game completion counter" that takes quests, minibosses, memories and the Hyrule Compendium into account would have been better IMHO. Or at least reducing the value of each Korok Seed so they don't account for literally three quarters of the total.