Meaning – What Does ‘It’ Mean in ‘That’s Not the Half of It’?

It doesn't mean it's an important thing; in fact it's sort of the opposite. What Ronan means is that he wished they learned more than "a bit", but he's glad they're at least learning something. He might have said instead "Well, that's better than nothing."

This is generally used when you wish something more/better than what is happening were possible, but are accepting what you can get. For example:

Jim: "Did you get everything we needed for the party? Sally really wanted those special crackers she likes."

Mary: "They didn't have those, but I did find paper plates with unicorns on them!"

Jim: "Well, that's something. Sally does like unicorns."

Wherein Jim really wishes Mary had gotten the crackers, but is pleased that at least something Sally likes will be present.

I think both of your suggestions sound a little off. I'd suggest

Not likely=

(1) I probably haven't finished my homework.

(2) I don't think so. (with a heavy emphasis on think – to indicate sarcasm, as mentioned in The Photon's answer)

However, I must ask: Did this question come straight from a test? Or did you make it up, or alter it somehow?

It seems unlikely that the phrase "not likely" would be used in the first person, not if we are talking about something that isn't in the future. The word "likely" is used to express a high probability. Therefore, if you ask me whether or not I've finished my homework, either I have finished it, or I haven't – there's no "likely" involved, because there's no uncertainty involved.

I could see the phrase not likely being used in this context (future tense):

Do you think you'll have your homework finished by 10 o'clock?
Not likely. (Meaning: "I probably won't.")

or this context (third person):

Do you think Ariana has finished her homework?
Not likely. (Meaning: "I doubt that she has.")

However, it's very hard to imagine me using "Not likely" as an answer to the question, "Have you finished your homework?" Then again, perhaps that's the point of the question; if it's meant to be an incorrect answer, maybe it's not supposed to sound interpretable.