Hi Song English. This is a good question! The way the writer uses 'Come to think of it', would sound strange to someone attempting to read it literally.
1) I agree with Adrian, but would say sentence 1 is grammatically 'acceptable', opposed to 'correct'.
In current United States english, 'come to think of it' is used when someone draws a conclusion about a fact or set of facts. They realize something after thinking about it, or reflecting on what they know.
You specifically asked what 'it' refers to. It refers to a CONCLUSION which is drawn from two implied facts. 1.1- He and her are distant relatives. 1.2- Because they are on an island, many other citizens are ALSO distant relatives. 1.2 is the 'it', or the 'conclusion' that is realized when the character/writer 'comes to think of it'.
In the second part of your question 2a,2b,2c are all correct, and all acceptable in common English. Yes - 2a, 2b, 2c would all have the same meaning.
I hope this helps!