Why does the concept of prime, primality only apply to multiplication and division?
One does not have to assume that they do...
Any discussion about what primes are should also mention what irreducibles are and what atoms are. They often get lumped together because for things like the integers, they amount to the same thing.
All three conditions have roots in lattice theory, and so you would probably be interested in this wiki.
There, in a lattice (or a join semilattice, at least),
$x$ is prime if $x\leq y\vee z$ implies $x\leq y$ or $x\leq z$;
$x$ is irreducible if $x=y\vee z$ implies $x=y$ or $x=z$; and
$x$ is an atom if the lattice has a least element $0$ and there is no $y$ other than $0$ and $x$ such that $0\leq y\leq x$.
Notice there are two ingredients: the partial order and the join operation. The partial order determines atoms (if they exist) and the join helps assemble them into other elements. The existence of atoms, and whether or not they generate everything in the lattice, and uniqueness of representation are all fundamental questions for these topics.
That's why you see these definitions on the same wiki page:
A lattice or is called atomic if for every $x\neq 0$, there's an atom $a\leq x$; and
atomistic if $x$ is the supremum of atoms less than $x$.
The comments bring up that commutative monoids are relevant. How do they fit in? Well, with the commutative binary operation in a monoid you get an upper semilattice of principal ideals of the monoid where $(a)\leq (b)$ means $(b)\subseteq (a)$. It can be checked that it has least element $(1)$ and that $(a)\vee (b)=(a)(b)=(ab)$ works as a least upper bound.
Compare that to the definitions in ring theory used with domains:
$x$ is prime if $x|yz$ implies $x|y$ or $x|z$;
$x$ is irreducible if $x=yz$ implies $x=uy$ or $x=uz$ for some unit $u$.
(In integral domains) it's this passage from elements to principal ideals generated by elements that precipitates rephrasing $(a)=(b)$ as an equivalence relation between elements in terms of the elements and units. For a general commutative monoid you could very well just say "$a\cong b$ if $(a)=(b)$" instead.
The lattice-theoretic notions above all become classical topics in commutative algebra for factorization questions: atomic domains, factorial domains, and best of all unique factorization domains, like $\mathbb Z$.
And also, for your example of knot theory, I read that the operation of summing knots in 3-space creates a commutative monoid, giving rise to its own sort of lattice. I am not sure what the situation is in general... I am not knowledgeable about knot theory.