The three phrases all have different meanings. #1 says there's MORE to know than what you see. #2 is poorly written. Perhaps the intention was to say "it's not AT all WHAT you think it looks like". That would mean that it is DIFFERENT from what you see. #3 asserts that all appearances are DECEPTIVE. So that's the difference: "more" vs. "different" vs. "deceptive".

Another similar phrase "Don't judge a book by its cover." Both mean to not judge immediately because there are more things to learn about the person or situation.

Yes, "It's not all you think it looks like" and "Nothing is as it seems" can be considered equivalent to "There's more than meets the eye." Other similar expressions that convey a similar meaning can be: Things aren't always what they appear to be Don't judge a book by its cover What you see is only half the story The devil is in the details All of these expressions suggest that there is more to a situation, person, or object than what is immediately apparent. Basically you should not jump to conclusions based solely on surface-level observations.