While the narration claims this is a cryptic answer, it is more in the sense of being cryptic to the other animals than to the reader. Benjamin is the oldest animal and the reader can intuit from this that he has seen a lot of events on the farm that the other animals have not.
This is the meaning of "Donkeys live a long time". "None of you has ever seen a dead donkey," had a twofold meaning: in the first instance, it supports the original statement that donkeys are long-lived and in the second it implies that they are hardy and will survive and endure no matter what privations are inflicted on them.
The key to understanding what Benjamin is implying here is to situation the quote in the context of what he's being asked: is he happier now that Jones has gone? By refusing to answer in the positive, we can understand that he is not. By his statement about his long life, he is implying that he has seen other attempts at bettering the working life on animals on the farm and that they have not succeeded. By then stating his endurance he is, in fact, suggesting it will likely do more harm than good.
Benjamin is a curious character in the novel because almost all the other characters either represent specific characters from Russian communism (i.e. Napoleon is Stalin), or a particular social class (i.e. Boxer is the working class). It is not entirely clear who Benjamin represents. His long memory of what has come before suggest he may represent the older people of Russia. His clear intelligence and critical attitude suggest he may be a member of the intelligentsia. He may also be a member of the middle classes, educated but not powerful or interested enough to engage with the revolution.