Are you not very thankful to have such a fine place to live at?
—Jane Eyre
Being familiar with the expression "aren't you […]," it's quite strange to meet this one. Is it the expression used just in the writer's age, or is it still prevalent?
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Sign up to join this community"Are you not" is definitely a far less common phrase these days. It has largely been replaced, as you suggest, by the phrase "aren't you" and other similar phrases.
However, with that said, it can certainly still be heard and read from time to time. It is very appropriate, in fact, in many circumstances. It tends to sound very formal (even a bit snooty if used improperly), but can be used to put emphasis on the not.
A: Alright, let's go; it's time to leave.
B: Hold on just a minute!
A: What, are you not ready? It's been an hour!
Probably not the greatest example, but hopefully you get the idea.
For comparison, and because I like these, an Ngram showing the usage of "aren't you" overtaking that of "are you not" over the last ~250 years:
The Corpus of Contemporary American English shows 4188 instances of aren't you (411 for the years between 2010-2012), and 375 instances of are you not (42 for the years between 2010-2012).
Are you not worried that all the gains that have been achieved over the past year might be lost?
Are you not teacher Mbele's son?
Why are you not making loans?
Are you not is used less frequently than aren't you, but that doesn't mean it is not used anymore.
For comparison, this is what the Corpus of Historical American English shows.