Spackle will work, or you could fill the holes in with toothpaste. Or putty.. Just sand whatever you use smooth, and you shouldn't have any problems.
You might consider embedding drywall mesh tape in the joint compound (spackle) used to cover the joint, just as though you are finishing drywall.
Dante
I recently completed the final installation of my backdrop panels which were made from 1/8" thick hardboard. I primed both sides before I installed them to seal the hardboard from moisture. I used the method described in Jeff Wilson's book on benchwork construction for doing the joints in the hardboard, i.e., I used a backer board to which I glued (yellow carpenter's glue) and screwed both sides of the joint. After the glued had set (approximately 24 hrs), I used DAP brand vinyl spackle based on the recommendation of Joe Fugate in his scenery video. No joint tape was used on the joints. The vinyl spackle is more flexible than drywall mud and thus is more resistant to cracking. I had to put two coats of the spackle on the joints and screw heads to get a smooth coat. I sanded between the coats and after the 2nd. coat had dried to get a smooth finish. Since I had primed the hardboard before I installed it, I only had to spot prime the spackle on the screw heads and joints. In the several months since I completed the spackling, I have seen no signs of cracking at the joints. I should say that my train room is in climate-controlled space in my basement.
Bob
For what it's worth, I used Behr brand Enamel Undercoater Primer & Sealer White No. 75 from Home Depot to prime my hardboard. I used the Behr brand because I was using their flat wall paint for my sky blue color. I found that it took 2 coats of the primer to keep the dark brown color of the hardboard from showing through. A friend of mine used Kilz primer and I believe he found that it also took 2 coats with this product. I applied the primer with a 9" Purdy brand 3/8" nap roller. Immediately after applying the primer while it was still wet, I went over the primer with a 6" Whizz brand high-density foam roller that I got at Lowes to get a very smooth surface. If you decide to use these foam rollers, you should wet them first with tap water and squeeze out the excess before you put them in the primer. I use them only to smooth the primer surface, not to apply it. If too much primer gets on the roller as I use it to smooth the surface, it will start to slide on the surface. When this happens, I roll the roller on a piece of dry paper towel to get off the excess primer. Also you should be aware that as you use them, the primer will start to harden on the end of the roller and this dry primer will come off in pieces and become embedded in the primer coat. To reduce this problem, I wrap the roller in wet paper towel and aluminum foil between uses. When the dried primer starts to accumulate on the end of the roler, as it will, I pitch it and use a new roller.
Hope this helps,