As a personal preference, I like Angel and Cyclops in a deep prussian or midnight blue rather than a simple gloss black. The Bolt, Widow, and Panther have always properly read as black to my eyes because, of course, they would be. The dark pools of ink that are almost always present on the characters help hold that impression. 

Maybe because I encountered Cyclops in a Marvel Triple Action reprint early on in which George Tuska left the body open in most panels, Cyclops has always read as a deep blue. Very dark, to be sure. Almost black, but not quite.

Storm's Cockrum costume without the blue highlights has always properly read as black to me. How Jim Lee and artists of his era ever saw that as white with deep, pooling shadows is a mystery to me. Shadows do not work like that against a white surface. (Similarly, they don't really do that against red either as they seem to with Wood's DD, but there at least the red had a darker value, making it still "translate" as possible to the eye.) It's just weird that somehow Storm's appearance became so badly misinterpreted (and I say that with no less than two gleaming pearl-white Storm action figures right within my line of sight. I seriously feel the need for a "correctly" colored 10-12" version of the character in the room.)

There's also the fact that comics are largely about color to consider. Those blue highlights which all-too-quickly morphed into blue costumes are more colorful and engaging, for the most part, than plain black alone would be.

Those characters like Kirby's original X-Men and Havok who were usually drawn in a flat  black without many highlights successfully translated to readers and follow-up artists as black. Those characters who wore shinier black costumes had to be drawn with constant dark shadows moving across them in order to preserve any sense of the original intent. Once Ditko stopped putting in the inky shadows on Spidey's costume, Spidey went blue and was a more colorful, merchandising-friendly character afterwards.

Would the Romita-Spidey we see on bedsheets, Underoos, and cans of Crazy Foam be as successful with the blue sections inked in?  Maybe. But we know that the blue-and-red look has done very well for the character and Marvel in general.