You're exactly right, Wes - the pocket eliminates the need for the daisy chain for most people.

The daisy chain appears to be oriented toward something Jimshaw has correctly talked about a lot: mission hardware. If you're going to be using the pack for climbing, the daisy chains could be a must-have feature for hanging climbing aids and ropes where they're easily accessible. Likewise, I suppose, for photo gear (like tripods?) that you might want easily accessible, or that won't fit easily inside the pack.

But, if you're "only" going backpacking, they're normally not needed. I've never used them when I had them (though I never cut them off, either - too much trouble to save an ounce or two on a 5 or 7 pound pack.) Like you said, I prefer everything inside the pack or a pocket - nothing to fall off, or get caught on trees and bushes. Also, there's nothing like a full water bottle swinging around on a carabiner to make the pack ride really poorly.

If you do have something long that won't go in the pack (for example, a closed-cell-foam sleeping pad), you can simply lay it across the top of the pack, between the pack and top pocket, and use the "floating" feature of the top pocket to secure the pad in place. Tent poles or fishing poles would go on the side of the pack, under the compression straps and into the side pocket. Again, the daisy chains aren't needed.

My guess? You'll never even think about wishing you had daisy chains.