I had two bolts that went through the luggage rack, up through two opposing lug nut holes...I drilled a hole in the end of one of the bolts, large enough to get a padlock through.
This setup was a TOTAL p.i.t.a. to un-do & remove, so I went back to the drawing board & re-invented it.
Now I have a gigantic 1 1/8" bolt with a 2" threaded section of 5/8" bolt welded to the head, that goes through the center section of the rack. (held on w/ a large washer / nylock nut)
This protrudes up through the center of the spare & is held down by an extra large washer I made out of 1/8" steel daimond plate, a large fender washer, lock washer, & mondo-gigantico wing nut I had fabricated by welding two 8" long pieces of 1/2" steel rod to opposing sides of a 1 1/8" nut.
I had a loop welded on one end that I run a chain through, then down through the spokes, under the luggage rack, & back up through the spokes with a larger lock holding the whole works together.
If they want my spare, they're gonna have to work on it awhile & destroy some stuff to get it. (unless they have a bolt cutter or mini grinder )
Doesn't matter what you do, if someone wants something of yours, & is the type of good-fer-nuthin' P.O.S. that would rather steal than work, they'll probably get it...unfortunate, but true.