I heard an interview (of sorts) with Ernie Gutierrez where he said that the absolute best way to store a cue is standing up vertically, put together, away from any exterior walls (less chance of moisture getting into the wood). He also recommended taking them out and playing them every few weeks because the wood will age, and resist warping, better if it's "worked out" now and again.
That said, put together or broken down, as long as they are stored straight up and down and in a place of fairly consistent temperature/humidity, they should be fine.