I would guess they would either transform more often depending on how much longer the moons are in the sky for (ie, if they obit close together and maintain the same speed, not much time difference, if they orbit on opposites sides of the planet, twice as long.)

Also if there are two moons in the sky at once, you could easily use that as an excuse to change their powers in interesting ways, for example making them more ferocious, more muscular, more beastlike. Expanding on that, you could make the transformation even more intense if there were many moons...