It is not something I would plan on letting happen regularly, but at the same time is also part of the battery calibration process you should be doing every so often - every six months or so depending on how hard you are on the battery.
The theory is that if you completely discharge the battery by letting it run out completely, then recharge the battery back to full, it gives the meter a more accurate reading of the power remaining in the battery (and helps remove against memory effects - this an issue with li-ion?)