There's a few options, which I'll use your examples to illustrate.
We were supposed to fight our way through a complicated maze of sewers
to get to this treasure vault we inherited, and instead the warforged
used his trusty crowbar to break open a grate and then we took a
shortcut past all the monsters.
This one is pretty easy. Put the majority of the treasure in the vault itself, and not on the monsters on the way. You get the treasure for completing the job (which was to get to the vault) rather than for killing everything on the way. Thus, it no longer matters how you deal with the encounters.
In the more general case, encounters can be designed such that there are rewards for not killing things.
Future Plot Hooks
That time when we were underground and we ran into a bunch of Gnolls,
and they didn't attack, and we didn't attack, and then they just kinda
left after a while, because really, who wants to attack adventurers?
That other time we encountered a couple of goblins in a muck farm
(don't ask), and instead of killing them all, we asked for directions
because, hey it turns out our hobbit speaks goblin.
Congratulations, you are not a party of murderhobos. As a DM, what I see as a result of these two situations is future plot hooks.
- The Goblin farmers may come to you for help later when they're having a problem, because you speak their language and were friendly. Muck farmers probably can't afford to pay you, but there is likely loot involved in solving their problem.
- The Gnolls may go on to cause problems elsewhere, and you could get paid by a town to make them go away.
- If you keep showing restraint, word can get around among that you have a knack for dealing with the more monstrous races peacefully. There's good money in being hired as diplomats to resolve disputes between the "civilized" races (Humans, Elves, etc) and the "other" races without it turning into outright war. Or maybe two human towns need you to help them keep a situation from turning into a war. (In my current game, we had an entire session devoted to brokering a peace treaty between two towns. It was awesome.)
There's organizations out there that like a thoughtful, less violent approach. The Church of Rao would be one such group, and they might seek you out to hire you because they think you can handle things without it turning into a bloodbath.
The Merchant Business
There was that other time where a living spell wandered into the section of the compound we were in, and instead of fighting it, we
locked it in a magical vault. Because it was attracted to sound. And
vault doors squeak.
I'm not sure what a living spell is, but it sounds valuable. Any Wizards want to study one? Any traveling menageries or carnival acts want to put one on display to wow the crowds? You've got it trapped in a vault, sell it to someone that wants such things.
Better Living Through Crafted Items
This one is on the players and not the DM, although the DM can encourage it. If the DM wants you to have a certain power level in terms of items but you have less money than expected, one option to deal with that is to get your items for cheaper.
Among the myriad of plot ways to do that, the non-plot way is to have someone in the party take an item crafting feat. For the price of a feat and some XP (some of which you earn back anyway when you lose a level from it as you gain XP faster if you're lower level than the rest of the party), crafted items cost half as much. Wealth goes a whole lot further when your armor is half price.
Now, item crafting feats have some problems, and there are ways the DM can help with that. The ones I use to encourage it are:
- Increase the speed. Normal magic item creation is 1000gp per day of value. That works very badly when you need to make swords for an entire party and it's going to take four months. Dramatically increase that amount.
- Allow the XP cost to spread around. Normally the XP cost is borne entirely by the item crafter, but it's more player friendly if you allow the person getting the item to bear some/all of the expense. That means your actual crafter has to spend a feat, but doesn't also have to fall behind in levels. I do this only with PC crafters, because the NPC crafters "don't want to give a discount on their livelihood."
The end result is that you simply need less wealth in terms of gold to spend to get equivalent levels of power, which means you can be behind the wealth by level chart and it won't hurt at all. You can also use downtime to make spare items, which you could sell for profit if you own your own shop or something (as my PCs do).
Also: the WBL chart is itself a guideline anyway. If you have skilled players and a strong party, you can deviate somewhat from it and not have problems.
Tell the Players To Get More Money
This one is something of a cop-out, but the DM can simply tell the players "you're going to be too poor for what's coming if you don't go kill some stuff." The players can respond to that by going off and doing a side quest to loot an otherwise pointless dungeon for extra gold.
The players are free to ignore this advice until they actually run into trouble, of course.