I'm glad you asked, little filly. The truth is that ponies' appearance is not mutable by emotions, nor is it merely stagecraft to communicate ideas to the viewer.
To find out what it is then, we have to look at the similarities between the aforementioned situations. I'll look at them one by one.
When the ponies lost their color in Return of Harmony, this wasn't due to any mere emotion or fleeting feeling. This was due to the complete and utter disappearance of that pony's element within the pony. This is different from the pony being sad or angry throughout the course of the day, and is far more akin to, in modern psychology, various mental disorders of the day, including depression - or in spiritual terms, it would be the hell state.
Judging by the fact that this is the first time we see this draining of color or anything similar in the Equestrian universe, there are some interesting facts we can derive, such as that while Equestria is obviously not perfect, it does lack the mental disorders that plague modern society to such an extent, that when a pony descends into that state, it is a serious thing indeed, requiring direct action from the Princess of Equestria, but I digress.
A counter-argument to this hypothesis may be cranky, in that he was chronically unhappy, but there is an explanation for this. Cranky never understood the magic of friendship, and as such, was unable to experience the total loss of the elements of harmony like the mane 6 did. This hypothesis, however, does call into question my previous hypothesis that Equestria was indeed a happy place lacking disorders such as depression, but I digress.
The second point of OP is that the mane 6 changed during the crystal heart thing, which better supports OP's polymorphic theory, though can be explained in that the crystal heart was powered by a lot of love and unity, which I would still say is different from emotions triggering it, in that the love and unity felt by the crystal ponies elevated them to a new level of consciousness - not just a temporary feeling. Again, they experienced thousands of years of apathy - this crystal coat appeared as a result of the sudden