Totally agree with you about LOTR! Great example of some klunk being good sometimes. Same with the Demogorgon shot in STh.
Whirlwind can be really klunky sometimes, but it's definitely by design. The playfield is cramped with shots and posts close to the flippers, the tornado target in the center launches airballs everywhere, and the stand-ups on either side of the right ramp ricochet quickly down the middle. Hitting the side ramp rewards you with a ball plunked directly onto spinning discs next to an outlane or right above the flipper gap.
I feel like Stop-and-Go style games can be klunkier without it being a drawback as long as the klunk adds to the funk when incoporated into the design. WW has two large rubbers on either side of the lower playfield to help you regain control and bouncing into the Cellar scoops during the chaos gives you a quick break before a safe-ish feed back to the flippers. It's obvious that Lawlor understood how to encourage players to at least try to control the ball and make shots just through the geometry of the game.
I've often heard Iron Maiden and Batman '66 described as klunky too. I don't necessarily disagree, but they're two of my favorites and I think it's interesting that their playfields are at opposite ends of the design spectrum. Elwin continually nails the Lawlor cramped layout theory of klunk and horizontal motion whereas Gomez gets his klunk funk with tighter shots further away from the flippers on an open playfield so that any miss has a good angle towards an outlane.