1. It seems that he is pale.
2. He seems to be pale.
-------------------------
Q1: In Sentence 1, what is the part of speech of 'that he is pale'? Is it a subject complement? Or is it a noun clause, which is a real subject?
Q2: What is the role of 'It' in #1? Does it refer to 'that clause'?
In 1, the clause "that he is pale" is a noun clause.
http://www.k12reader.com/term/noun-clause/
The initial word "that" is the indicator, although other initial words can be used.
And yes, it's a subject complement.
"It" is one of those impersonal pronouns that is serving as the subject of the sentence. It cannot refer to the clause because the clause hasn't been spoken/read yet. Antecedents are words that occur earlier in a sentence.