Yes, "mystery" in the sentence "The disappearance of the colony is a great mystery" is functioning as a predicate noun. A predicate noun, also known as a predicate nominative, is a noun that appears in the predicate of a sentence and renames or identifies the subject. In this case, "mystery" renames or identifies what the subject, "The disappearance of the colony," is. It states that the disappearance of the colony is a great mystery.
