A short answer to your question is yes, most contractions make speech less formal; however, some of your examples seem to mix formality and informality and perhaps the answer you are looking for is not so simple.
Ending a statement with something like "is she not?" does sound formal to most native speakers, not because there is anything particularly exceptional about the statement, but mainly because any word or phraseology that has fallen from everyday speech tends to sound formal. For whatever reason, few people would speak like that informally. It would be more common to hear such a qualification in a court of law when a barrister was seeking confirmation of someone's statement (eg "you stated that you were out of the country at the time of the offence, did you not?")
However, there is nothing particularly formal about saying "She is not here" as opposed to "she's not here" or "she isn't here". The contractions are probably more common, but no more or less formal. Again I would have to say this is all down to usage - if a form of phrasing is in everyday use then there is nothing particularly formal about it.
I do not really know what you mean by "double informal" - it sounds like you are trying to break down a single sentence into parts which are formal and informal, but really speech as a whole is either formal or it is not. When someone mixes highly informal speech with a formal phrase it is generally deliberate and for effect. Speech that does not fit the general pattern stands out. Someone may use a formal mode of speech in a formal setting for comic effect (eg "It's your turn to buy the drinks, is it not?")
Also, not all of your examples mean the same thing.
She is here, is she not?
She is here, isn't she?
These two mean the same thing. They imply that the speaker believes "her" to be here and is either seeking confirmation for that belief, questioning a suggestion to the contrary, or perhaps showing a measure of doubt.
She isn't here, is she?
This doesn't have the same implication; in fact it is the reverse. It suggests an initial belief that "she" isn't here.