Based on Spotrac, the Jays have him for 5 years $92.4M, so it's like $18.5M on average. I don't know the exactly $/WAR calc these days, but I suspect he only needs to be a 2.5 WAR player to justify that contract.
If he was a 95 wRC+ bat, he's probably a 4-5 WAR player and thus would have been providing excess value. I suspect that Jays felt there was a 50% chance that would happen. There's simply always a probability it doesn't happen, but even with a limp d*ck bat, he's a 3 WAR shortstop, which isn't a terrible outcome. I get the claims that you don't pay for defense, but a slick fielding SS impacts and helps all of our pitchers too. His base running / stolen base ability is also something the Jays have lacked for years.
Honestly, if this is your biggest complaint about Atkins, he's doing pretty good.