It is better to say "I am looking for a pair of black shoes". Why? The shoes are black, and the rule is that a modifying word or phrase should lie as close as possible to the word being modified. That is the proximity rule. I mean, guideline.

Either way of asking for the black shoes is correct. They are pretty much interchangeable. In this case since shoes is plural saying how much are they is more correct. But when you walk up to a counter, if you said "how much is it?" they would think you mean how much is the price or the cost; price/cost being singular.

I'm looking for a black pair of shoes. How much are they?