The natural thing to do here is to replace the intervals $[1,n]$ (and $n = |[1,n]|$) in the definition of $d(A)$ with a sequence $F_n$ of subsets of $\mathbb{N}$ which is multiplicatively asymptotically invariant (or, in other words, a Folner sequence for the semigroup $(\mathbb{N},\cdot)$). For an exploration of this idea, as well as applications, see for instance this article by Vitaly Bergelson:
EDIT: One particular example (mentioned in the article) is to take $F_n$ to be the set of all positive integers which can be written as a product of powers of the first $n$ primes, where the powers are allowed to be any non-negative integer which is less than or equal to $n$. The motivation for choosing $F_n$ this way is that just as $1$ generates the additive semigroup $(\mathbb{N},+)$, the primes generate the multiplicative semigroup. Think of balls in the corresponding Cayley graphs with radius getting larger and larger. The article contains many other examples of such $F_n$, and each of them gives a notion of "multiplicative density" by setting $d(A) = \lim_{n \to \infty} \frac{|A \cap F_n|}{|F_n|}$ (if the limit exists. Otherwise one usually considers the limsup and liminf).
