I fail to grasp this. Do your PCs never go to cities? Or come up with a plan that you failed to forsee? You've never had to come up with a baker, or street urchin, or sewer worker on the fly? You've never had PCs ignore your planned dinner with the Mayor to go off to see the swamp orcs you never got around to fully detailing.
First, my prep is to make a bunch of characters. The session is improvised largely by finding excuses to use them. So if my players go to a city, they find the people that I have ready.
Second, if I need to, I improvise a character, pause for a moment, and then come up with detail.
Third, even if I don't know everything about an NPC, I operate under the assumption that there is something to be known. If some random swamp orc attacks the PCs, he has a reason for doing so. If he gets in a dire situation, I have no difficulty considering what that reason might be, and then figuring out whether he would retreat, surrender, or try some desperate tactic.
Likewise unless your world only contains a dozen people your NPC cannot be as fully fleshed as a decent PC as you simply don't have the time to fully develop all the hundreds, or thousands of people/monsters they might bump into in a years campaign.
I think of D&D like a TV show in real time. One of the similarities is that there may only be twelve viable characters in play during a session, just like a show can only cast so many speaking parts. I simply try to avoid using the other background players unless I need to.
But it's also important that I have the philosophical stance that all those scenery characters are in every way the PCs' equals. If I'm watching something on the screen, and I get the sense that the main cast and the other characters aren't following the same rules, that's one of the fastest things to take me out of it. Some people don't mind the notion that the heroes shoot straight and the stormtroopers don't, but that is completely unacceptable to me (and my players). By the same token, I would not use a morale rule that did not apply equally to PCs and NPCs (which as I said would cause my players to rebel against me).
In any event, as has been mentioned, morale listings are valuable even if the mechanical system is completely ignored. Even a plain language listing with no supporting mechanical system but a single line entry like "Pathetic/low/Normal/high/fanatical" is still a tool to inform you what, in general, this race is meant to be like.
At that point, it's basically fluff. Fluff is okay, but I don't use it much. I just wouldn't use this type of rule in any form, that's all there is to it. I don't see the need for it. If it was included in an unobtrusive, optional way, I wouldn't revolt against our WotC overlords, I'd just be mildly disappointed because it reflects a philosophy I don't agree with.
To each, his own.