Although I agree with your assertion on the level that they're not really my idea of good adventures, I strongly disagree that verisimilitude should take precedence over hard-to-justify-yet-fun dungeon encounters. White Plume Mountain-style dungeons with weird challenges may not make sense, but done well they're generally a lot more fun to play than many of the "cabinet contents" style dungeons which make perfect sense and have bedrooms and latrines for everyone, but someone forgot to add the weird magical fountains and riddle traps-style stuff that makes D&D enjoyable to play, rather than a yawnful tour of real estate with little to do but fight (or indulge in the usual "disguise", or "negotiate with the factions" cop-outs which are available options in most any adventure). If the encounters and locations of the Fighting Fantasy game books all "made sense" in the currently accepted wisdom of D&D, they wouldn't have been nearly as popular, fun or successful as they have been. Funny thing is, few people seem to even realise what they've lost."Lich Queen's Beloved", however, is a wonderful module, full of many uses. It is not just a module, it is a useful piece of campaign material. While it is a very flavorful dungeon, it has a full context with which to place it in, and many more ways for it to be utilized, other than a simple dungeon crawl. The inhanbitants are well developed, have reasons for being where they are, and the whole of the dungeon is designed with both logic and care. Exploring the Lich Queen's palace reveals a lot about the Lich Queen and her servants, and has a distinctive feel. The palace feels like her domain. Compare that with "Heart of Nightfang Spire", which has whole sections that don't make a lot of sense, and comes across as just plain silly at times.
Again, although it's nice to have verisimilitude, sacrificing the fun for sake of realism is not everyone's idea of a good D&D game, IMO. Mind you, it has to be worth the sacrifice in the other direction as well...compromising verisimilitude for sake of poor quality, unfun anachronisms is bad design as well.The Storm Lord's Keep, on the other hand, feels like an excuse to use Force Dragons and Mithral Golems, as some sort of silly anteing-up to Epic. Encounters feel 'dropped in' and players don't really affect the environment much. The Lich Queen's fortress, quite simply, made sense. And the more you learned about the queen, the more you understood it. The Storm Lord, on other hand, is just some guy with a magic item that affects the weather and a beef with folks on the ground down below. Lich Queen's Beloved makes assumptions about high-level characters powers, understands them and challenges players to use them to the fullest. Storm Lord's Keep seems designed merely to thwart them, so that they'll stay in the maze and keep looking for the cheese.
I think it depends. In the case of Return to the Temple of Elemental Evil, if viewed as a regular module as opposed to a "DM's playground" there was really no excuse I could see for not building in a strong, compelling reason for the PCs to want to keep at the monolithic challenge the main dungeon presented. Some suggestions were made, but none seemed compelling enough to warrant the scope of the ensuing crawl. On the other hand, if RttToEE were viewed more as a plotless DM's playground setting ala Keep on the Borderlands, there was no need for presenting a compelling hook - it's more, here's the keys to the car, do what you will with it.And ultimately, a module has to, IMHO, either allow enough space for a custom plot hook, or do more than simply assume that the PCs will come along for the ride "simply because they're heroes". It doesn't have to be much, you understand, but more than simply "come on, play along, even though it makes no sense in the context of your characters." That can be tough, sometimes, but most modules in Dungeon show that it's routinely easy to do. Simple things beyond "we'll pay you" and "hey, you're heroes, right?"...or leave me space to do it myself, and offer some suggestions.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.