Hi, kupo! Have no fear, Dungeon Hero X is here!
It is added at the end of many of the sentences spoken by moogle characters throughout the series, usually as a means of emphasizing said sentences. Some games briefly mention a moogle language formed out of various permutations of "kupo". This could explain why "kupo" can be added to the end of spoken (and some written) sentences, despite the tone and actual context.
In some games, moogles can only speak in "kupos", while in other games, they can speak human language but still begin or end their sentences with the phrase, and even use them as an adjective. Square Enix has not revealed the actual meaning of kupo, if such even exists. Sometimes, when the moogles are relaxing or in surprise, they also use "kupo"; it has also been used as a term of endearment and a derogatory term.
When moogles first appeared in Final Fantasy III, they used the word "nya", which is the Japanese onomatopoeia for a cat's "meow". This was changed in the later games to "kupo". In the Nintendo DS remake of Final Fantasy III, "nya" was also changed into "kupo"; this could imply that "kupo" (and "nya" by extension) are simply noises the moogles make, or some form of a verbal tic.