Two reasons; cost and location. Sunk relief was less time consuming, and therefore less expensive, than raised relief. As you can imagine, its easier to smooth a flat surface with a few holes in it than to carve around intricate raised relief to create a flat background. You can find examples of just how cheap sunk relief could get by googling "Naga ed-Der stelas," which are a group of often very poorly crafted stelas from the first intermediate period, all of which are sunk relief or, if really cheap, just painted.

The other reason an artist might choose sunk relief is the location. For example, a dark tomb where torchlight is used frequently might benefit from sunk relief, which would cast realistic shadows on the art and make it appear as if the art is moving. On the other hand, a well-lit temple wall would probably benefit more from raised relief, which would show prestige.