NiCad Batteries which are still used but more widely used before Li-Ion took hold will last longer if completely discharged. Li-Ion is the opposite, they will last longer if you keep them topped off, most info advises not letting them go below 3v and most regulators in modes have a cutoff around 3.2 - 3.3v.
I wouldn't go overboard, sounds like you're using a slim battery that has low voltage pertection but if you aren't going to be using it for a while it's a good idea to top it off if it's been used or even stored for a long period of time.