Like most respondents I lock the canoe(s) to the rack crossbars with a cable. If, as usual, we have two or more canoes I lock them not only to the rack but to each other, sometimes with a second lock & cable. Belt & suspenders; if a thief cut the lock around the roof rack bars they might find two canoes locked together unwieldy obvious (and noisy) to make off with, or simply get off the racks.
“I don't know the type of establishment you will be staying at but if you talked with the staff at the more reputable ones they may, after a certain hour, let you park close to the main entrance under the lights as long as you're not blocking the place for emergency vehicles”
I do not care for motels, even decent ones, but sometimes it is the best solution for the night, and I request a room “Down and out, up front”. That is motel speak for a 1st floor walk out room, up near the motel office and lights. With the truck parked five feet from the bedroom window I sleep better; parked in the dim back lot near the dumpster, in a second floor room distant from the truck, not so much. Not just for the canoes but also for the thousands of dollars worth of more easily stealable paddling and camping gear.
I have never had an issue using that technique in a motel room stay. I did stay in a hotel on a non-paddling trip and parked the truck in the hotel garage. When I went into the garage to leave the next morning I saw the truck in the garage and thought “McCrea, you dumb arse, you never shut the driver’s door all the way”. And then, truly a dumb arse, thought “And you parked on a pile of broken glass”
Cleaned out, even took my speakers and dirty laundry. No more hotel parking garages for me. Well, once. The missus planned a weekend getaway, with a hotel stay. The parking garage, the only option, was not tall enough for our van with canoes on the racks. The hotel staff allowed us to store them overnight in an unused conference room.