You have to think about how it's spoken, and naturally, English tends to an alternation of stressed and unstressed syllables. (In this respect, it has something in common with Portuguese, which I see is your native language.) So when you say something like "they are not coming", then you have to ask what the important thing is. That word will wind up stressed. Also, the first syllable of "coming' attracts stress. Then the contractions tend to "eat up" what is left over. Sometimes that favours a particular expression and sometimes it doesn't. Thus: - "THEY aren't coming" -- but the other guys are - "They're NOT coming" -- even although you just said they would be

Both ways are grammatically okay, but you're right in saying that the first options are slightly more colloquial and informal. So in daily conversation I would say "it's not" or "you're not" frequently but in more formal conversations or in written form I would probably choose to say "it isn't/it is not" or "you aren't/you are not."

I'd never really thought about it before, but as an American native speaker, I frankly don't see any difference at all. For example, "They aren't coming to the party" or "They're not coming to the party"; or, "It's not too cold to play outside" vs. "It isn't too cold to play outside." Your question is a good one, but I see no difference between the two, either in terms of meaning or formality.