If you don't mind a variable speed from your motor, then powering it with a variable voltage from a battery of Li-ions is OK. However, you need to consider what happens at the maximum and minimum voltage of the cells. Your particular motor application (which you don't give us the detail of) will control what's important.
There are two issues with providing too high a voltage.
(1) The motor goes faster than you want. This will mean it runs less efficiently, and wears out more quickly.
(2) Motors are usually rated to be able to switch on, without the current surge they take when stationary being so large as to demagnetise (read 'destroy') the motor. Applying a higher voltage than rated could do this, unless you also use active current limiting.
Too low a voltage will mean the motor may go too slow, or not be able to draw enough current to develop the required torque.
If you need to provide a precise 48v to your motor, then there are two easy ways to organise your cells.
(a) Make the highest voltage from the battery < 48v, and use a simple boost converter. Uses fewer cells. Results in higher currents in the battery wiring for the same motor power.
(b) Make the lowest voltage from your battery > 48v, and use a simple buck converter. This will also allow you to control the motor down to zero speed, and to limit the current easily avoiding the switch on surge. These two factors together with the lower battery current will often make this the preferred choice, if you're happy with the larger battery.
(or c) Have the voltage range from your battery overlap that of the motor, and use a buck-boost or other converter that allows you to convert up or down in voltage.
