Isn't Waterdeep (or any big city) not another maze? And if they kicked the hornets nest, wouldn't getting to other locations not also provide hurdles when the enemy also knows the city well or better then the party? Facing another group of thugs suddenly becomes a LOT more dangerous when they alpha-striked the first group and the next group is between them and their supplier of healing potions... I think it's about educating players in a different play style, for if you let this happen continuously without consequence, nothing will ever change and no matter how you redesign it, they will continue to behave this way.
The difference is narrative vs location-based play. A dungeon is location-based play: you're goal it to explore the dungeon and achieve some goal (loot all the treasure, find all the kidnapped villagers, disrupt the cultists, slay the dragon, etc). Generally, encounters are structured by rooms and the rooms are arranged so that the players must encounter so many of them before they reach their goal. In that scenario, attrition is easy to measure: I have 10 rooms and six encounters, I know my players were be involved in most or all of them and thus I can balance for a longer adventuring day. Likewise, my players know there is going to be multiple encounters and will pace accordingly.
Narrative gameplay, where play is designed around encounters happening in a time-based or cause-and-effect order, is murkier. For one, there isn't as much of a time-based pressure unless the DM instills one. Investigating a mystery has no set window of time unless the DM places a ticking clock (find the killer before he strikes again). Second, there is much less emphasis on constant danger. Waterdeep has dangers, but its still a major civilian city. Players don't worry about random monsters, rarely worry about ambushes, and very rarely worry about traps and hazards costing resources. The fact that players can often take short or long rests in the safety of the inn which is usually a short walk away, not a miles-long trek back. Finally, narrative gameplay is often reactionary to the players, so its much harder to judge how many encounters before they figure out the Count and his men are behind the poisoning and they may approach the Count daisy fresh or after several encounters with his thugs. Hard to judge how difficult to make the encounter with the Count.
I'm using an urban/mystery style adventure because its perhaps the most easy example of an anti-dungeon that is still a classic model of D&D play. There are plenty of other examples.
To be honest, it's not that the system 'fails' outside of the dungeon, it's the DM that fails. You either do one encounter by design in an urban, woodland, etc. setting or you do multiple, and each choice is on the DM. And if you only do one encounter, that's not a problem imho, due to the alpha-strike nature of the characters, they can handle a pretty big encounter, just be sure you know what that is exactly before you start throwing heavy artillery in their direction. But you don't have too stick with only one encounter outside of the dungeon...
Again, its more a question of controlling how many encounters. For example: a three-day trip to explore the woods to get to a dungeon. Typically, random encounter checks aren't rolled more than 1-2 times per day. So if the PCs do have an encounter on the road, why aren't they novaing? What are the odds they will encounter two, let alone 6-8, random encounters in one day of travel? If so, each day to the dungeon WOULD BE a dungeon! That's Final Fantasy levels of overworld encounters!
Think of it as an action movie: In this scene the heroes just used all their ammo and handgrenades to take out the gangmember hideout, but they called for reinforcements, which show up and chase the heroes.
A fine scenario, but how many sets of reinforcements can a hidden cult or a crime syndicate call on? And if they had so many resources, why are they attacking black-ninja style in waves?
That's what I'm getting at about D&D's resource management being based on multiple small encounters PER DAY. If you don't have that many encounters in the allotted timeframe, you run the risk each encounter can be overcome with superior firepower the encounter design system didn't account for. (Mearl's point). However, its nearly impossible to get 6-8 encounters per long rest UNLESS you design under a very specific set of restrictions (PCs are forced to fight multiple encounters, have limited access to rest/recharge, and on a strict time limit) and the only place that makes sense without feeling arbitrary is The Dungeon. Once you leave the dungeon, the DM must force those limits to remain or the potential to nova (and thus ruin anything resembling balance in the encounter creation rules) goes up.
What OP is discussing is the idea that resources be built around Per Encounter rather than Per Day management, so that the number of encounters a day must have is no longer forced. It doesn't matter if an adventure has one encounter or eight, the PCs will bring the same amount of energy to each.