If a self-map $σ\colon \mathcal{X} \rightarrow \mathcal{X}$ has a dynamical zeta function with nonzero radius of convergence $1/Λ$ and the Cesàro mean $B$ of $ \# \mathrm{Fix}(σ^k)/Λ^k$ exists and is positive, we show a large deviation principle for the number of prime orbits occurring in the decomposition of a general orbit of length $\leq X$ (an element of the free abelian monoid generated by the prime orbits or, equivalently, a prime orbit of a finite multiset in $\mathcal{X}$) with speed $B \log X$ and universal rate function equal to that of the Poisson distribution with unit mean. We also show a large deviation principle for more general strongly additive functions. The proof uses asymptotic results on the total number of general orbits, as well as a weak analogue of Mertens's second theorem, that may be of independent interest. The theory applies, for example, to endomorphisms of algebraic groups over finite fields, additive cellular automata, and automorphisms of some solenoids.