I've worked in hotels for over 10 years and can say that you should never have any problems vaping in a non-smoking hotel room. I not only smoke in the rooms at the hotels I work at but also behind the desk in front of my bosses.
The only way your going to get knocked for smoking in a room is if there's ash, butts, cig burns, and/or the room completely REEKS of cigarettes.(Not a problem with vape!) Basically the hotel isn't going to risk a chargeback unless there is undeniable proof that you smoked in the room.
The only way I can see this happening with vape is if you have a flavor that smells exactly like cigarette smoke and it somehow traps itself in all the fabric. I've tried tons of flavors, both tobacco flavor and fruties, and nothing really smells like cigarette smoke nor have I come back to any room I've vaped in(for hours sometimes) and thought it smelled like the vape I was vaping earlier.
Maybe there are some flavors out there that do get in to fabrics and what not but i haven't come across any. And unless the room smells EXACTLY like cigarette smoke, you'll be fine. People leave rooms all the time that smell like body odor or other nasty smells and they never get charged anything. Hotels have procedures in place to deal with rooms like these like carpet cleaning and washing all the drapes and stuff.
The reason smokers get charged is because it's a choice you make to smoke in the room and it is more common than the other stuff like B/O which doesn't happen very often. It harder to get out and the room is often down for at least one night for deodorizing (lost revenue). It also affects the allergies of people coming into the room after you if it's not eliminated completely(possibly more lost revenue). I'm sure everyone who started vaping can notice how you can smell a smoker a mile away now! This is the same reason people who sneak pets into non pet rooms get charged.