"It" is not doing the judging, but the person who is making the statement is making the judgment. With this prefix you are showing that you have made a judgement, and then you are making a statement of your opinion.
If you make a statement of fact such as "he does not comb his hair", then it is assumed you know this for a fact. By prefixing this with "judging by his appearance..." you are showing that you don't know for a fact he doesn't comb his hair, but you have made that judgement based on his current appearance.
The problem with your example is that it is repeating itself unnecessarily:
Judging by his appearance, it is clear that he doesn't comb his hair.
The words "it is clear" is really doing the same job as the words "judging by his appearance" but in a more assertive way. "Judging by" carries a sense that your statement is based only on what you can see, but perhaps there may be other facts to consider. On the other hand, if something is "clear" then it is obviously apparent; so with these words, you are saying that his appearance makes the fact clear.
I would expect to hear either:
Judging by his appearance, he doesn't comb his hair.
It is clear (by his appearance) that he doesn't comb his hair.