I'm very much into taking care of my weapons, sanding and oiling them monthly.
I think the best way to keep the weapons warp free is to prop them against a wall as vertically as possible. The horizontal racks are good for display, we have them at our dojo but all the weapons are warped because of that.
Traditionally, since bokken is supposed to be treated like a real sword at all times, you should keep it handle up and blade down. However, since I found out that it is not really a sword but just a piece of expensive wood, keeping it blade down may cause the point to break or be damaged in transportation, which can be quite expensive knowing the crazy prices of good quality bokken, so while in the carrying case, I keep it the opposite way, handle down, despite the fact that I won't be able to draw it fast enough in case of an unexpected attack