First of all, it sounds strange. I don't think that the word probably fits in the sentence since must have implies that it was the case that he was an excellent student. Probably implies that it was likely the case. It didn't have to be. So, one should not use probably and must have in the same sentence. It should be either
- He must have been an excellent student.
Meaning that it is the case that was he was an excellent student. Or,
- He was probably an excellent student.
Meaning that it is likely the case that he was an excellent student.
If however, this is an example of what someone (like a native speaker) might say, then I accept this. I can imagine someone saying this. The reason I can imagine this is because it sounds like hedging. Meaning that as the speaker utters He must have, something changes his mind, and realizes that maybe must have is too strong, and softens his statement by following up with probably.
In one sense,
He must have probably been an excellent student
means that it was (or likely was) the case that the student was excellent.
For example, suppose you meet this person, and he seems sharp. You didn't know him in college, but you imagine that he was an excellent student. So you might remark to someone else that
He was sharp. He must have probably been an excellent student.
In another sense, if you claim that the site states
Perhaps, he was not the most excellent student.
Then this sounds like an example of sarcasm. Like maybe two teacher friends are talking about a third teacher who is irresponsible and is a terrible teacher.
They speculate about his student days and say
He must have probably been an excellent student.
They imply that he was likely a terrible student too.