It's a little thing called "artistic license". Makuta in the movies seems to have taken some inspiration from his original, infected appearance, in addition to the then-new set of him. Rest assured, though, that the Makuta in the movies is based on the set and not vice-versa.
It's very silly to suggest Makuta was "meant to look" how he appeared in the movies, when the movies' purpose was to sell sets...
Too many colours can be a bad thing, not just with pins and axles, but in general, especially when you know the character isn't really meant to look that way. For instance, Makuta in the movies is shown as almost completely burnt metal, yet the 2003 set features colours from solid black all the way to bright red.
The movie characters and sets have to resemble each other or otherwise how would the former promote the latter?
What I'm saying is that it seems strange that Makuta's set is such a jumble of colours when his media portrayal is nothing like that.
Almost all sets back then were a jumble of colors, and frankly the variety of color on the Makuta set may have been the best way to simulate the "infected" color variation he had become known for.
And in terms of my argument re: colored pins and axles, my point was that from the start Bionicle had a technological/industrial aesthetic, carried over from Throwbots/Slizers. Lots of pistons, gears, etc. Some of the closest things we have in real life with that sort of aesthetic are vehicles and industrial robots, which generally favor function over form. They may feature decorative elements (like the Kanohi), but in most cases they won't bother painting all the nuts, bolts, and other functional parts or parts that may need to be replaced in the future. Similarly, I think that Bionicle sets need not have monochromatic connector elements, especially when those elements are so insignificant in the model's overall color scheme. And if the connectors are overly prominent, then the problem is with the set's design and not with the colors of the elements themselves.
As for MOCs, I understand that they may often want to use certain colors of pins for aesthetic purposes, seeing as they have no reason to adhere to Bionicle's own design principles. But older pins and axles are plentiful when you know where to look, so if the colors of those elements are that essential to the MOC you're working on, there are avenues for obtaining the ones you want.