No, the howl casualties don't count towards CR for exactly the reason you mentioned. It's not in the rules. Besides, the howl comes in the shooting phase, unlike impact hits which are calculated in the combat phase.
I tend to agree with you about the banshee's usefulness. Most of my regular opponents either don't mind a few casualties (skaven, goblins) or are ItP (CoS, various Chaos, banner of "Screw You Vampire Counts" or some such).
When I do take them, I like to take two, along with spirit hosts. For those foes who are vulnerable, three ethereal units, two of which can cause big hurt, cause a lot of problems.
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