Satisfiability modulo theorem solvers are often a good choice for expressing mathematical problems that would otherwise end up using one-hot CNF encodings. A key insight is that with CNF and DPLL-based solvers alone you're limited to what unit propagation can discover efficiently. At a higher level of abstraction there are theories of numbers and sets that can be used to prune the search space before selectively applying a SAT solver to more appropriate subproblems. That's what SMT gives you, along with more expressive power and a much more pleasant language in which express relationships.
But if you're stuck with one-hot constraints with no associated higher level math problem, there are more efficient ways to encode onehot constraints that require only a linear number of new clauses to express the relation instead of the usual quadratic increase. See
Efficient CNF Encoding for Selecting 1 from N Objects by Klieber and Kwon.