this was our discussion before:
http://forums.azbilliards.com/showthread.php?t=76952&highlight=storing+cues
Apart from humidity, extreme temperatures, & the very nature of the wood as a non-stable material that contribute to warping, gravity can also cause the cue to warp.
TO sum things up, in a vertical position, the entire cue is being pulled by gravity in only one direction. If it's in a horizontal position, the entire length of the cue is being pulled at different rates (just see what happens to the telephone/electric lines between poles). More so the mass of the cue is not evenly distributed due to its tapered construction.
IMO, it's still better to store your cues vertically inside the case if you're gonna store it for a
LONG time. HOWEVER, it's a good practice to move your cues from time to time so that the wood fibers are not
STRESSED (imagine yourself standing up on both feet or putting more weight on the other foot for a long time, you'll feel the stress in a few minutes unlike when you move from time to time, you'll be able to stand longer). Again, just MOVE the cues, I'm not saying that you have to rattle them inside.

Another reason for moving the cue(s) is that the case is not really standing perfectly vertical unlike when the cues are hanging like a pendulum...
I guess one of the reasons why RIP's cues warped inside his dealer case is that there's more STRESS to the shafts' tip area coming from joint as there's more mass present there... just like an inverted pyramid or standing on your hands. There'll even be more pressure to the tip area if the case's interior doesn't have a snug fit feature (like that of memory foams). If the tube has a snug fit on the shaft, especially shaft is stored tip down, then it's almost like hanging the cue as the opening is hugging the thick joint area resulting to less, or none at all, to the thinner tip area.
Of course it takes TIME for gravity to really act on your cue. If you use your cues often like several times a week, then I guess it doesn't really matter much if you cues are stored horizontally or vertically.