Yes, this can be done. We've gotten this question a few times, so it sounds like we could probably make this clearer to users as to how this works.
We separate the property setting vs what you ask on the website forms, so you have more flexbility. That is, we let you include the check boxes on the forms even if you specify at the property that this property doesn't allow pets/smokers because some hosts want to ask anyway (so that they know this person is a smoker or this person wants to bring a pet). With this, you potentially have more info at your disposable, should you want to go out of your way to, for example, reinforce your smoker/pet policies or even check to make sure a pet was not brought on the trip (in case the traveller tries to sneak Fido into your rental without telling you). Does that make sense?
To remove these checkboxes, you go to the booking page in our advanced Page Layout Editor, hover over the form where those checkboxes are included, and click on the settings for that form widget. You'll see the show/hide settings there. Here's a quick gif of my turning these off on my own website (below). Remember to save the page at the end (the green button in the bottom left of the screen).
I am having trouble embedding the animated gif, but try clicking on this: https://www.screencast.com/t/flS0PlN3L4zC