Yes, avoiding deep discharges is highly recommended, as it will provide longer cycle life.
Most Li-Ion cells (LiCo, LiMn, and LiFe) like to be stored about half charged (ideally 40% SOC). I wouldn't see that as a problem though. Charge your drill up, use it, then preferably, check the pack voltage so as not to put it away with too little charge left. If you needed to use it right away, after it had been stored, it would work for a while, as it'd still have some charge left. The nice thing about Li-Ion's in general, is they have very low self discharge, comparable to LSD NiMH's, or better. Pulling your drill out of storage shouldn't really be a problem, unless it's been years or something. It's not a bad idea to check on the packs voltage once in a while anyway, so there shouldn't be any surprises.
One thing about Li-Ion's you have to remember though, is that they degrade whether you use them or not. Still, newer Li-Ion cells and especially the LiFe's, have longer storage life than older cells. If I could get at least 5 years out of a drill pack, I'd be ahead of where I am now. I think with proper storage voltage maintained, not keeping the drill in a hot car etc., it'd be possible to do even better than that. I have flashlight LiCo Li-Ion cells that are 5 years old, and still @ 80%+ capacity, and they get used regularly, so......
Dave