The simple reality is that its pretty hard to finger strike someone in the throat or in a "soft spot" if they're punching you in the face. Especially when you've never actually trained yourself to use it in that situation.
You are rite when you say that for most to deliver nukite blows could be hard and tricky, add very hard to a target in motion. Indeed for most persons they would never trade a chance to deliver a regular punch to deliver a finger poke instead. And like you said, it has also to do with another mentality and aproach in your way of fighting and strategies and thats not a thing that happens tru night from day ofc (conditioning). But remember by no means that doesnt invalidate the uselfuness of those techniques.
Shihon nukite in the solar plexus really its not that hard coz most people doesnt defend belly/abdomen lower region of the body like they would apply to defend their face and the neck. Besides that, shihon nukite can gives you more range than a single punch: 3 to 4 inches more generally, and usually thats enough to catch a fleeing face/neck or torso in a place that the regular punch will just miss.
Add to that: the head alone can go back to retreat and evade a strike in a more wide angle that the neck or the torso can without moving your stance. So the neck and plexus will be in range for hits more often than you think.
In most cases ofc, i believe, IMHO, its a strike better suited for when the opponent are not very fast and mobile so you actually can hit in with more safety what you have aimed for. Preferably you will make a devastating effect to apply that (in the neck-throat or plexus) even before the fight begun, if you have that chance, and that i can say to you with 100% sure. Ofc one have to make decisions. Its truly a dangerous technique, i would recommend others to use it in a life or death situation but not in a school fight with your coleague coz you looked so much to his gf.
The better question is why were none thrown in the first place? If its such a high percentage move, we would have seen it being used in such fights to devastating effect.
No event promoter wants to justice govern, public opinion ending their show coz people are getting killed. They will always make conventions and rules to prevent that. You talked about UFC's. All i can say its no body was permitted to hit the neck with such strikes even when it was pride or war of worlds and no matter how much they claimed about being a no rules fight event. Rules always were there you can be sure of that.
The times those techniques were delivered in old kumites in my country, the effects were bad, those still banned from the sport. I can try to research about that when i have the time coz i found this an interesting subject. I know that at least 2 athletes got dead but really dunno if they were by nukite strikes. The only case i know from a nukite blow it was a person that have experienced next to death when his upper trachea collapsed in regional kumite event, and if it was not for a doctor putting a tube on his lower part of the throat for him to breath the guy would just passed away. The doc said that generally only 5 pounds of force could brake the thyroid cartilage an the larynx.
Again, MA aiming for SD and MA for sports can not be measured by the same definition and strategies. Sure they have a lot of techniques and even strategies in common but still its a lot of difference regarding training and conditioning mentality.
I can give you a practice example of that. The time you realize that some of the things you are doing exaustively at the dojo will not serve for you in SD situations maybe you can review some of your points and try to aproach shotokan in a different manner. Not that commercialized manner that doesnt have any focus in SD but only for sports.
I used to practiced some strategies with a BB BJJ work coleague , always with SD in focus not sports. In a particular training session i convinced him to use cervical colar, torso protection gear and protective googles in the training coz i would aim to hit a lot his neck. I was using mostly shihon, tate, omote and ippon nukite at him when i was standed up. And i have managed to hit his neck and eyes with effectiveness more than one time.
When he dropped me to the ground (most of the times mounted on me) i used ippon ken at his neck coz its a short range strike and i have hitted manny times his neck. He is a competent jiu-jitsu fighter he knew that he had to defend his neck but his training conditioning was almost to defend from arm bents and locks he wouldnt expect several ippon ken and hiraken hits at his neck while i forced my way out to a ground and pound. His neck were way too open to attacks when he was trying to grab and lock my arms and hands. Punches from the ground when we are being mounted are not effective coz we cant turn our hips properly to give the punch any expressive power. Its completely uselles to punch when you are not up there mounting and punching with gravity force added. From down there and with such short range and small space you only rely on your fingers and fore knuckle blows on the soft spots when you think of strikes. I watch MMA sports and when i see someone punching while on the ground my mind its already focused on another strategy.