These examples are all valid; adjectives and articles can be used to modify colors.
The usage is somewhat confusing, as we normally think of colors as adjectives, not nouns. However, they can be used as either. For example, in this sentence:
The car was blue
"blue" is an adjective modifying car. Here, on the other hand:
Red is my favorite color.
"red" is a noun and the subject of the sentence. Usually the context makes it clear which use is intended. As you noticed, however, there's a somewhat confusing usage where the noun form is used to describe the color of some other object:
His cloak was a dark blue.
As you pointed out, the article "a" should only be used to introduce a noun phrase. As such, we know that "blue" is here being used as a noun. This makes the sentence grammatically correct but nonsensical, as a cloak and a wavelength of light are obviously not the same. This construct does not follow common grammar rules, but is itself fairly common, especially in prose or dramatic writing. The best way to interpret it is to simply insert "the color of" before the described object:
(The color of) his cloak was a dark blue.
This form of the sentence is rather wordy and awkward, but carries the actual meaning intended by the original sentence. When using the indeterminate article "a", it's hard to justify the construct from anything except an aesthetic standpoint. As you can see in Alan Carmack's comment, though, there are circumstances where using similar constructs with a color and a qualifier can deliver useful information.