Spillways are simply a water management tool. Some ponds have pipes as the primary spillway. All ponds should have an earthen emergency spillway. Some ponds have only an earthen spillway, depending on watershed size. A pipe gives better control where you want the water to go, especially if you want to use the water elsewhere. Plus, you can turn a pipe on, or off, with a valve. An earthen spillway only spills.
Structural integrity won't be compromised if the dam is properly built. Bentonite is used to seal porous soils. Porous soils are not necessarily bad construction soils. They just don't hold water.
If I were you, I would learn as much about my dirt as possible. Find out what's in it, how compactible it is, and how much clay content there is.
Then, decide what to do.
