The book Stream Ciphers and Number Theory by Cusick, Ding and Renvall is devoted to this topic, stream ciphers being one kind of symmetric cipher. I give some examples from there that are not that well known.
One security measure for a keystream output by a stream cipher is its linear complexity, i.e., the lowest order linear recurrence which it satisfies. This is usually obtained by the Berlekamp Massey algorithm applied to the output, and must be high with respect to the period of the sequence, since Berlekamp Massey is an efficient recursive algorithm.
The sphere complexity of a sequence is a generalization; it is the minimal value of the linear complexity, if an adversary can flip $k$ bits of the sequence?
A basic result that is used in this text is the following.
Let $N=p_1^{e_1}\cdots p_t^{e_t},$ where $p_i$ are $t$ pairwise distinct primes, and $q$ is a positive integer (power of a prime) such that $\gcd(q,N)=1.$ Then for each nonconstant sequence $s$ of period $N$ over $GF(q)$,
$$
L(s)\geq \min\{ord_{p_1}(q),\ldots,ord_{p_t}(q)\}
$$
and
$$
SC_k(s)\geq \min \{ord_{p_1}(q),\ldots,ord_{p_t}(q)\},
$$
if $k<\min\{WH(s),N-WH(s)\}.$ Here $WH$ is the Hamming weight of the sequence $s$ $L(s)$ is its linear complexity, $SC_k(s)$ is its sphere complexity under $k$ bitflips, and $ord(\cdot)$ denotes multiplicative order.
Also note that one can define a power generator in $\mathbb{Z}_{pq}$ via choosing an initial setting $a_0 \in \mathbb{Z}_{pq}$ and letting $a_{t+1} = a_t^d \pmod N.$ For $d=2,$ this is the Blum Blum Shub generator, and has some nice security properties if $p,q$ are both congruent to 3 modulo 4, though a bit slow to be used directly as a keystream in modern symmetric cryptography. One can prove that if we only take the least significant $k$ bits of each $a_t$ as an output block of bits, provided $k\leq \log N,$ breaking this keystream (determining the initial loading) is equivalent to factoring $N.$
The classical theory of binary Linear Shift Register Sequences and their nonlinear filterings, as pioneered by Golomb in his book Shift Register Sequences and extended further is another example, however this is not explicitly or deeply number theoretic in nature, in my opinion.