As someone who plays Stoneforge Mystic in Zoo, the biggest problem is actually getting the equipment destroyed, either in response to the equip activation or in response to you attacking. Using Stoneforge to put the equipment directly into play at EoT is often the best play, because then you can untap and equip, then re-equip if they Plow your guy. I mean, yeah, this lets you save on mana at the expense of life, but if you're connecting with a Jitte-wielding Tarmogoyf, the mana saved is actually not really as big of a deal as it seems at first blush: whether you have two mana up or no mana up is irrelevant as the game is effectively over against a lot of decks. Jitte-Goyfs are that good.

Furthermore, sometimes you will activate an equip knowing full well they have the removal, simply to bait the spell out; losing your Nacatl and not having anyone carrying a Jitte is fine if it draws attention away from your Knights and Goyfs. There are plenty of situations where it is correct to sink mana into sacrificing a guy because it maximizes damage in the medium and long terms. Situations like this are ideal for Misstep, but depending on the matchup Misstep itself might not be worth boarding in; this trick is cute, but sometimes brute force is just better, and there's nothing you want to take out because it reduces your ability to brawn your way through situations. I realize that sideboard cards are all "context-dependent," but I try to select cards that are good across the widest variety of contexts while also being clearly superior to cards in my main in those same contexts. Against a Bant deck, for example, there's nothing I'd want to side out for Misstep as my maindeck is already quite solid, and I'm fine throwing away a Nacatl every now and then to force the opponent to discard a StP.

That said, Qasali Pridemage and Krosan Grip make investing in equipment in the first place incredibly unattractive, and neither of those are Misstep-able.

As for other Zoo decks, I don't know. Yeah, not having to face Vial is nice, but you're beating the kind of decks that pack Vial on a strategic level by having better guys and a high density of removal. Vial is their highest-profile weapon to fight you, but you already have incidental removal for it in the form of Pridemage and possibly GSZ. As for Top, well...you're probably already running Krosan Grips if you're expecting a lot of Top matchups, and in Big Zoo you've got GSZ for Pridemage on top of that, so I'm not really seeing the need to run Misstep over, say, Null Rod, which is better against Thopter decks and helps against combo and Affinity. And what is "medium" Zoo supposed to beat? You have fewer trumps than Big Zoo, and less speed than Cat Sligh - what's the attraction of that kind of build over the others?