It's a joke. Only some of the Latin words imported into English retain their Latin plurals (antenna, antennae -- for example, and even that is getting less and less common). Bonus is usually pluralized by an English rule, as you observed, 'bonuses.' But in the Latin from which it originated, the plural would be 'boni' in the nominative.
This is not unlike the old joke: "A classics professor walks into a bar. His nose is bleeding and his clothes are torn. He says, 'I just got jumped by a couple of hoodl
i!'"
Of course, any students of Latin hearing this joke are expected to call out, "That's 'hoodl
a!'" because although 'hoodlum' is not actually a Latin word, if it were it would be of the neuter gender.
Deset Gled said:
My classics trained fiancee blames this on 1) bad latin and 2) people who want to sound smarter than they are.
Sounding smarter than you are is what studying the classics is for. But psedo-Latin plurals are way too quotidian for anyone who takes pretentiousness seriously. Now, pseudo-Latin inflection by case, that's where you're not just trying to pretentious -- you've actually invested ranks in it.
And yes, it does occasionally happen in the real world, too. For example, the true latin-based plural of octopus is really octopodes, not octopi.
Both the word and the inflection rule are Greek. It just happens to come to English as something that looks like a Latin noun.