Exponential time is not required for finding the requested probability. In fact, only linear time is needed, as we will see below.
First let's define some additional notation. Let $X = (x_1, x_2, \ldots, x_n)$ and $Y = (y_1, y_2, \ldots, y_n)$ -- that is, two $n$-tuples of our variables. Let $\mathbf{1}$ denote an $n$-tuple of 1s, $ (1, 1, \ldots, 1)$. And let $S_n$ denote the set of all possible $n$-tuples of $0$ and $1$. In CS literature, the elements of $S_n$ are sometimes called "strings". If $\sigma$ is one such element, we write $\sigma(k)$ for its $k$th component.
In this new notation, the task is to compute $\Pr(Y = \mathbf{1})$. We can marginalize out the configuration of 0s and 1s on $X$ as follows:
$$\Pr(Y = \mathbf{1}) = \sum_{\sigma \in S_n} \Pr(Y = \mathbf{1} | X = \sigma) \Pr (X = \sigma).$$
From the prompt we know that each $x_k$ is 0 or 1 with equal probability, so $\Pr (X = \sigma) = 2^{-n}$ for every $\sigma \in S_n$. Additionally, for any given $\sigma \in S_n$, we know that $\Pr(Y = \mathbf{1} | X = \sigma) = \prod_{k=1}^n p_{k,\sigma(k)}$, since the probabilities $p_{k,\sigma(k)}$ are independent. Combining these observations, we obtain
$$\Pr(Y = \mathbf{1}) = 2^{-n} \sum_{\sigma \in S_n} \prod_{k=1}^n p_{k,\sigma(k)}.$$
Our next step is to show that we can factor the left-hand side of this equation as follows:
$$\sum_{\sigma \in S_n} \prod_{k=1}^n p_{k,\sigma(k)} = \prod_{k=1}^n (p_{k,0}+p_{k,1}).$$
We prove this inductively. When $n = 1$, both sides are $p_{1,0}+p_{1,1}$, so the base case holds. For the inductive case, we assume the $(n-1)$th case and write the $n$th case as
$$(p_{n,0}+p_{n,1}) \sum_{\sigma \in S_{n-1}} \prod_{k=1}^{n-1} p_{k,\sigma(k)} = (p_{n,0}+p_{n,1}) \prod_{k=1}^{n-1} (p_{k,0}+p_{k,1}).$$
Both sides simplify to those of the above identity, respectively, so the identity is proved.
This leaves us with the result that $\Pr(Y = \mathbf{1}) = 2^{-n} \prod_{k=1}^n (p_{k,0}+p_{k,1}).$ For a hash table representation, look-up times are $O(1)$ for each $p_{k,0}$ and $p_{k,1}$, so we can compute this product with a simple for-loop in a runtime of $O(n)$.