What are the pros and cons of natural deduction relative to Hilbert-style systems?
From Wikipedia, I get the impression that natural deduction proofs tend to be shorter and closer to how humans do it. If so, why do some proof-checkers, like Metamath, use Hilbert-style systems?
It is hard to give a comprehensive answer, but the Metamath Proof Explorer(MPE) has some relevant things to say as to why they chose to go with a Hilbert-style system in terms of its strengths and lack of downsides. I will quote them at length so that this answer is more self-contained.
The appendix on Traditional Textbook Axioms of Predicate Calculus explains:
The "Weak Deduction Theorem" section of the page on the "Weak Deduction Theorem for Classical Logic explains why they do not (directly) use the standard deduction theorem from natural deduction/Gentzen-style systems:
It is notable that the ease of constructing proofs in natural deduction can be recovered essentially completely in a Hilbert-style system like MPE's. Basically, just write the hypotheses and conclusion in "deduction form" where there is an extra "$P\to$" in front of everything (a trick that may have been first pointed out by Mario Carneiro). This allows you to use Hilbert-style translations of the rules of natural deduction, such as the ones listed in MPE's "natded" list of translations. For a lot more commentary on this approach, see MPE's page "Deduction Form and Natural Deduction". Most of that page might be helpful, but I want to highlight a bit from the section "Strengths of the current approach":