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As far as I know, primitive recursive arithmetic can be characterised as the initial category with finite products containing a parametrised NNO. Likewise, Godel's System T is the initial cartesian closed category containing a NNO. We can say these things because the respective doctrines are essentially algebraic.
Is it also true that Heyting (resp. Peano) arithmetic is the initial Heyting (resp. Boolean) category with a parametrised NNO? Also, can anything similar be said about second-order arithmetic?
There isn't really anything out there about the categorical semantics of second-order logic. My first guess would be that, like first-order theories are indexed posets with quantifiers to substitution, second-order theories should be indexed first-order hyperdoctrines.
Those are fun questions! I can't help you with them, but I hope someone tells us some answers.
Maybe a bit orthogonal to your question (and/or telling you things you already know), but one can ask which functions on naturals are representable given a NNO + some further structure. Afaik, in a monoidal category a NNO gives all primitive recursive functions, and under suitable conditions you get all partial recursive functions (aka computable functions. See these slides by Phil Scott http://www.site.uottawa.ca/%7Ephil/papers/Lambekfest2.pdf and/or this paper by Gordon Plotkin for more https://link.springer.com/chapter/10.1007/978-3-642-38164-5_21