They both can be used. "In the dark" is a little stronger, implying we know little or nothing. "very unclear" is not quite as strong - we may know something, but many things are still unknown. However, this is a subtle nuance. You could interchange the two in most situations.

DanShui, 1.this matter is still in the dark. "In the dark" refers to a state of ignorance or a state of secrecy. If the matter is in the dark, then it is a secret matter. People can be in the dark about a matter, which means that they are in a state of ignorance concerning a matter. -We are still very much in the dark about the matter. -Such transactions were often made in the dark. (in secret) 2.this matter is still very unclear This means that the matter is not easy to understand, or that the someone is not certain about the matter -Police say thay the motive for the attack is still unclear. -He is a little unclear about the matter.