Mold is the least of the problems as a good alkaline cleaner will make short work of killing and removing it. Deposits in the lines, or, Beer Stone is the real concern. Be sure that your lines are spotless if you are going to let them dry. any solids left in the line will form hard deposits that can be near impossible to remove once set. they produce every kind of side effect fro0m off flavors to foamy beer. they will proggressively get worse too. It starts out almost unnoticable (think about your siphon hose.....does it have a permenant smell of beer?). every time you dry a line that is not perfectly clean it will build the beer stone. Not cleaning your lines regularly will cause stone build-up as well (every two weeks is an industry standard).
We used to have jockey boxes for St. Patricks Day events we would store all year. I would load up the lines and coils with PBW and let them sit the entire year. A flush with fresh water, and we were off and running a year later. the only thing I would have to change was the o-ring in the faucet. It would tend to be rather soft and breaking up after a year. The beer line was perfect, no stone, no odor, no discoloration.
I had a couple systems we set up where lines were not used all the time (i.e. only on nickle beer night, or fight night etc...). The owner of the establishment insisted we kept the lines dry. We had many instances where beer stone, and/or oxidation of the chrome fittings created some "issues" on the finished product. If you are certain the lines are spotless, drying them is o.k. If you use BLC or PBW or B-Brite, leave the lines full and you will have no problems. It's up to you, just be warned. Beer stone that sets for a few months is a pretty stubborn animal.
