It will shorten the coil's life a bit, but probably not much. This relay is rated for automotive use, and a car's electrical system runs at about 14V when the car is running and the alternator is charging the battery, so 16V isn't too much more than that. How much it will shorten the coil's life is hard to say.
Something you could do is put a resistor in series with the coil, to drop the voltage that appears across the coil to 12V. As I mentioned in my review of this relay, the coil's resistance is 90 ohms, so if you want to drop from 16V to 12V (that is, if you want the resistor to drop 4V), then use a resistor of 30 ohms. However, 30 ohm resistors aren't always available, so something close would work: 27 or 33 ohms would be fine (you don't need to be very precise here). As for the resistor's power rating, it will consume about 0.5W, so make sure it is rated for at LEAST that much power (standard resistors are only rated for 0.25W).