The issue here is that WebStorm generates internal warnings using JSHint, but this internal mechanism is entirely separate from enabling JSHint under Settings/Languages & Frameworks/JavaScript/Code Quality Tools/JSHint. (If you enable JSHint there, you'll get even more warnings, it seems like JSHint is basically running twice with different configurations.)
You need to configure the inspections in Settings/Editor/Inspections, then in the list on the right, find JavaScript/JavaScript validity issues. That worked for me to remove the Chai warnings. (I am using the WebStorm 11 EAP at the moment.)