Using past perfect twice in a sentence and the difference between Had not and Did not

Hi,

Could you please tell me what the difference is between had not and did not?

Eg-

My friend told me he had failed because he had not studied.

My friend told me he had failed because he did not study.

Moreover, would the reported speech for the following two sentences be the same-

Friend: I failed because I did not study / I failed because I had not studied.

Reported Speech: He said he had failed because he had not studied.

Is it ok to use past perfect twice in that sentence or any other sentence for that matter? Does it not confuse the reader?

eg-

Friend: I was disappointed that I was not allowed to resubmit my assignment.

Reported Speech: He said he had been disappointed that he had not been allowed to resubmit his assignment.

Can't you just write it in simple past?

Sorry for asking too many questions and thanks.