In my work book I saw the sentence: 现在这个咖啡的颜色好一点，不是很黑
My question is: if 黑 (in 不是很黑) is an adjective, why it is used with 是? should it be 不太黑？
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In 不是很黑， 是 is used as a linking verb. In a negative sentence, when we have 很 modify an adjective, 是 should be used. E.g. 他不是很好，她不是很漂亮. Well, 他不很好 and 她不很漂亮 aren't natural.
However, without 很, we don't use 是 in such sentences. E.g. 她不漂亮, not 她不是漂亮. There's also an emphasis 是 and the position of 是 is moved to "before 是", like 是不 instead of 不是. E.g. 她是不漂亮. 他是不好. etc.
是 has many different meanings/usages, one of them is semi-equivalent to "be" in English. Just like "be" can be used with adjectives, it's perfectly fine to use 是 with adjectives, e.g., 咖啡是黑色的。
It is true that, especially in the presence of adverbs like 很/有点, 是 is often omitted, E.g., 咖啡很苦。However, even then you can still use 是 for emphasis or concession in an affirmation: 咖啡是很苦。In a negation, using 不是很黑vs不很黑 doesn't have any discernible difference in most contexts.
"很" is an adverb that means "very or too". Here it modifies the adjective "黑" (dark). You can think of this sentence as saying "现在这个咖啡的颜色好一点了，不是很黑 - "Now the color of the coffee looks a little better, (it) isn't(不是) very dark", or "Now the color of the coffee looks a little better, not(不) very dark".
"不是(isn't/not)很黑(very dark)" = "不(not)很黑(ver dark)". Similarly, 不是太黑 = 不太黑. Here, "是" can be treated as an auxiliary word that has no specific meaning/function, and can be eliminated without changing the meaning of the sentence.