It's not a problem for the battery. Lithium-ion and lithium polymer batteries are not shipped discharged - fully discharging either type of battery results in lower capacity and shorter lives - but they also do not self-discharge very quickly at all. They are usually shipped with only a moderate charge, and this is usually of maintaining the minimum voltage for up to a year of shelf time.
As others pointed out, it is always a good idea to check for problems immediately after you get a new system to make sure that the system is in fact what you ordered and that it works correctly.