I did the same on my trip. Cover the bike at night.
2012 Victory Cross Country Tour (Stage 1)
2011 Victory Cross Country (traded in on XCT)
2009 Triumph Rocket III Touring (traded in on XC)
1998 Valkyrie Tourer (Hydralocked - sold as is)
1966 Honda 305 Dream (for sale)
1967 Honda 305 Scrambler (project)
1982 Honda CB900 Custom (need to put back together)
Connie and I have spents many months touring on motos, both here and in other countries. I just quit worrying so much. I do have insurance and take anything valuable out at night. Have never had an issue, nor know anyone who has, although I'm sure it happens.
At most hotels, we have found you can park on the sidewalk, or out front of the office in a lighted area, which might help.
If you have a rack on the top case you could easily make up a coated wire cable (any hardware store) with looped ends and a padlock...lock the case to the bike. Not elegant but should help if really worried.
Also, how difficult to just remove the topcase and take it in the hotel/motel??
I've been on several long mult state trips when I had my Harley. There was a lock on the Tour pack to keep the honest people honest so I did not really worry. With the Vivtory Tour Pack costing so much and being very easy to remove from the bike I am concerned.
I don't want to carry around a bike cover because space is at a permium.
I took one of my bags off and had a closer look. You're right. There is a nut welded to the trunk bracket that I mistook for a bolt because there is one right next to it. It appears that if you get a long bolt and screw it into the bracket it disables the trunk release from being lifted. It also wouldnt have enough clearance to be removed with the bag in place. Now, I just have to figure out what size screw goes into the bolt.
2011 White XC with Trunk
OEM Bag Protectors
Cee Bailey Deflectors