For one thing, if you're running NP and Sub you would not have room for WoW. Secondly if it is running WoW then you would instantly know its running PS + Taunt and only has one attack in Shadowball and therefore can be more easily dealt with.As a side note, although I do run Chansey, Mismagius is a pain. There is NO counter to a Mismagius behind a Sub, and very few to those without one. Most of the checks can be crippled by a possible Will-O-Wisp, and those that aren't are maimed by -insert attack at +2 here-.
Ciccino does a number on Mismagius with Bullet Seed being able to switch in on NP or Shadowball and outspeed it, go through sub and if it gets the 5 hit combo, a KO. Rhyperior outright slaughters it with Rock Blast only needing upto a 4 hit.
Jumpluff, Alakazam, Whimsicott (if it drops to UU), Accelgor, Liepard all outspeed Mismagius and come in on the NP or Sub and Encore Missy through the Sub. Altaria or Tangrowth can easily come in on Missy, and steal all its boosts with Power Swap.
There are probably more methods of dealing with it I can't recall off the top of my head.