There is a Lucrezia Borgia event, part of the Women's History dlc. But she's only available as an advisor, I think.
There is also a Papal States event chain, called The Borgia Pope. This fires the event "Cesare Borgia", which gives you Cesare as a general (5/4/4/3). Then onces the Borgia Papacy event chain ends, Navarre (should it still exist at this point) gets an event that gives them Cesare Borgia as a general.
I will admit, the Borgia representation is kinda lackluster, especially because they were an interesting, if somewhat scandalous, family.