Do they have the same meaning?
I mean is there any difference between we are ready yet and we are not ready yet.
She has telephoned yet and she hasn't telephoned yet.
The latest examples you have given have completely different meanings!
We are ready (not we are ready yet) = We are ready now.
We are not ready yet = We are currently not ready but we will be in the future.
She has telephoned (not she has telephoned yet) = I have already received a telephone call from her.
She hasn't telephoned yet = I have not received a call.
The main difference you will note is that your original post involved a question, whereas your latest examples are statements.
In a question, both the positive and negative versions have the same
general meaning.
Have you found a job yet? = I want to know if you have found a job. This is an open enquiry and you really don't know the answer already.
Haven't you found a job yet? = I want to know if you have or have not found a job. Admittedly, the use of "Haven't you" suggests that you probably think the person hasn't found a job yet, but you're still asking the same general question.
In both cases, the responder can either say "Yes, I have" or "No, I haven't".
With your later examples, if you turned them into questions, you will see the same sort of effect:
Are you ready yet?
Aren't you ready yet?
Has she telephoned yet?
Hasn't she telephoned yet?
The only real difference between the two constructions is that probably, by asking "Aren't you/haven't you/hasn't she...?" you already have an idea that you know that the answer is "No" but you're not sure.