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4wd Hardware has (or had) a good one. There are hardshelled covers that cover the little trunk area, which can be made lockable. A 2-piece paddle might fit in there diagonally. One-piece, good luck.
Here's an example from Bestop:
I had one like it when I owned a Wrangler. I never put a paddle in there, though--I mainly used the hardtop and even when using the softtop I just cable-locked the paddle inside and turned on my antitheft system. Hardly theftproof, but good enough for grabbing lunch on the way home from an outing.
Smittybilt makes another steel trunk that, although more expensive, makes a larger storage area.
Barring installation of items such as the above, your best bet for an unlockable vehicle would be a combination of out-of-sight plus locked to the frame, probably using a long bike cable lock spiraled tightly around the (encased) paddle). Good luck coming up with a system.
I can hardly imagine paddles being the only thing valuable left inside the vehicle, and if there's other stuff too, Pikabike's idea is certainly the best one so far. On that note, I'm sure this is one reason that soft-top Jeeps have become incredibly rare. The hard-top covers are a lot more secure.
If it really is just the paddles that you are worried out, I might make a lockable wooden box with a very flat profile, or easier still, take a plank and add "stoppers" in such a pattern that the two or four paddle halves can lay against the board and can't shift around sideways or endwise (you could put two halves against one side, and the other two against the other side, but you could rig it up so the paddles can be stacked). The simplest way to lock the paddles in place would be with a long-shanked, adjustable padlock passing through the plank and around the shafts. For multiple shafts, even better would be some sort of bracket that you make yourself, with a padlock to hold it on the back side of the plank, but even a short-linked chain passing through holes on each side of the shafts would do the trick (the shorter the links, the more precise the tightness adjustment will be). Whether you use a flat, enclosed box or an open plank with locks and "motion limiting blocks" to keep the paddles in place, the device is then fastened to something secure with some steel chain (many SUVs now have cargo anchor points, but even the seatbelt mounts would be fine if they are reasonably accessible. I might still do what others have suggested, and put the thing on the floor with some kind of cover that doesn't look like it was put there to hide anything (like a crappy tarp and a few empty fast-food bags).
Edit: Here's another simple locking method to hold paddles against the plank. Install two pairs of angle iron that "reach up" away from the plank a distance that is higher than the thickness of the paddle shafts. For each pair, install a long-shanked padlock through matching holes in the angle-iron pieces (or take a bit more time and rig up some other hold-down mechanism that spans the gap between the angle-iron brackets which can be locked with a standard padlock). This would be better than the methods above for plank-mounted locking, because there's no need for the locking method to be form-fitting (saves construction effort or resorting to the use of adjustable chains), with the benefit that any number of shafts can be lain alongside each other between the angle-iron locking brackets. You could build the whole locking device in an hour or so (half that long if you or a friend has a lot of tinkering experience). By the way, the "plank" could just be half-inch plywood, since it's mainly the deterrent effect that matters.
Oh by the way, all connections should be bolted, through the plank, not screwed to it. Then you can "lock" each bolt by crimping the nut or deforming the free end with a hammer (use a second hammer as a small anvil).
A friend of mine has been carrying paddling gear, stoves, packs, tents, etc., inside the topper of a pickup, and for years the topper couldn't even be locked. So far, so good with that system. No doubt it depends where you leave the car too.