"If your hair is already wet" is the correct way, we use "it´s" to refer to a subject that "is there" but it´s too generic, you think about it almost in terms of "abstract" (something that is everywhere but nowhere in particular). That is, to refer to phenomenon of nature (mostly), to mark the existence of the subject: e.g. It´s raining.
So the sentence should be "but don't be surprised if your hair is already wet." (no commas here), since we clearly have a (concrete noun) subject in the sentence (hair).
Plus, we are stating that "don´t be surprised if" (so we shouldn´t split the sentence in two).