Your best bet is to only stay in motels where you have to enter from the inside to get to your room. This lessens the likelihood of someone trying to break in. Desk clerks are coached by thier supervisors very carefully on how to answer security questions. I worked for individual franchises for Days Inn and Hampton Inn. When you ask a question be very specific.
Someone is on the desk all the time and the police are good at patrolling.
This does not tell you if that motel has security it just tells you someone is watching the desk and the town has police. This will have to be a yes or a no and gives no room to get around the question. Not that I know of. This does not tell you what you need to know. I was raped while on duty at an individual franchise for a national motel chain.