Here is another NP-complete variation of the DFA intersection non-emptiness problem.
(1) Given a list of DFA's and a number $n$ (in unary), does there exist a string of length at most $n$ that is accepted by all of the DFA's?
Also, here are two NP-complete variations of the DFA non-emptiness problem.
(2) Given a 2DFA and a number $n$ (in unary), does there exist a string of length at most $n$ that is accepted by the 2DFA?
(3) Consider an infinite set of variables $\Sigma := \{ x_i \}_{i \in \mathbb{N}}$. A mask is a finite sequence of variables from $\Sigma$. Given a mask $m$ and a DFA $D$, does there exist a binary assignment to the variables from $m$ such that $D$ accepts $m$?
Update
The three problems above are all $NP$-complete. They are in $NP$ because they have polynomial time verifiers with polynomial size certificates.
Below I will add some justification for $NP$-hardness.
3-SAT is reducible to (1): Follows by essentially the same argument as in Theorem 1 from "Detecting patterns in finite regular and context-free languages". It's also worth looking at "The Parameterized Complexity of Intersection and Composition Operations on Sets of Finite-State Automata" where a related problem denoted by $BDFAI_R$ is investigated.
(1) is reducible to (2): By 2DFA, we mean a two-way deterministic finite automata. The following observation is sufficient. Given a set of $k$ DFA's $\{ D_i \}_{i \in [k]}$ with $n$ states each, we can construct a 2DFA $X$ with roughly $k \cdot n$ states such that $L(X) = \cap_{i \in [k]} L(D_i)$. Essentially, $X$ reads over the input string $k$ times simulating each of the $k$ DFA's one at a time.
3-SAT is reducible to (3):
Let a 3-CNF Boolean formula $\phi$ with $m$ 3-CNF clauses, $n$ variables, and $l$ literal occurrences be given. We construct a DFA with $O(m+n+l)$ states that reads in a sequence of $2 \cdot l$ bits. The DFA reads in one pair of bits for each literal occurrence. For each pair of bits, the first bit represents the sign of the associated literal (positive or negated) and the second bit represents the value assigned to its variable. The DFA accepts if all of the signs match the formula $\phi$ and if each block of three pairs of bits corresponds with a satisfied 3-CNF clause. Also, we construct a mask of length $2 \cdot l$ that makes sure that the assignment is consistent for each variable. Consistent means that all occurrences of the same variable are assigned the same value. The mask has $l + n$ variables where $l$ are used for the signs of literals and $n$ are used for the variables of $\phi$. In other words, $l$ are used for the first bits of the pairs and $n$ are used for the second bits of the pairs.