In the following answer, I assume that the question tries to apply $E_{in}$ as the test error rate and $E_{out}$ as the true error rate. The current question formulation is ambiguous on this issue.
The theorem application is wrong
The cause of the confusion comes from misapplication of Hoeffding's Inequality. Hoeffding's Inequality deals with random variables and probabilities. However the question's set up involves constants, for example, the statement $$Pr(|E_{out}| \geq \epsilon) \leq 2e^{-2n\epsilon^2}$$
doesn't even make sense as $E_{out}$ is a constant.
Starting from the beginning, what one version of the inequality states is :
Hoeffding's Inequality. Let $Z_1, \ldots, Z_n$ be random, independent random variables, such that $0 \leq Z_i \leq 1$. Then,
$$Pr(|\frac{1}{n}\sum_{i=1}^n Z_i - E(\sum_{i=1}^n Z_i)| > \epsilon) \leq 2e^{-2n\epsilon^2}$$
The inequality is a statement about probability that a difference between the RANDOM variable $\frac{1}{n}\sum_{i=1}^n Z_i$ and the constant $E(\sum_{i=1}^n Z_i)$ is larger than some value $\epsilon$.
The question seems to try to substitute the $E_{in}$ term as the random variable. That doesn't work because $\mathbb{1}_{h(x_i) = y}$ is not random - the question's author assumes that a set $\lbrace x_1, \ldots, x_d\rbrace = D$ is given as $h$ is defined on $D$. Also it's not clear how would the true error rate $E_{out}$ relate to that definition of $Z_i$.
To summarize, the statement
Then Hoeffding's inequality says the following:
$Pr(|E_{in} - E_{out}| \geq \epsilon) \leq 2e^{-2n\epsilon^2}$
doesn't even make sense.
Correct application
A correct application of the inequality would look as follows.
Let $h$ be a classifier defined on a finite domain $X$. Let $Z_i, i \in \lbrace 1, \ldots, n\rbrace$ be a collection of i.i.d. variables, such that $Z_i = 0$ if $h(x)$ correctly classifies a random sample $x \in X$ and $Z_i = 1$ if the classification is incorrect.
Note that $E(Z)$ is the true error rate of the classifier $h$.
You can check that all conditions of the Hoeffding's lemma occur. Therefore
$$Pr(|\frac{1}{n}\sum_{i=1}^n Z_i - E(\sum_{i=1}^n Z_i)| > \epsilon) = Pr(|\frac{1}{n}\sum_{i=1}^n Z_i - E_{out}| > \epsilon) \leq 2e^{-2n\epsilon^2}$$
If you were now to get a random sample of size $n$: $(x_i, y_i) \in D$, and calculate $h$'s error rate on that test data, then the theorem guarantees that the chance that your measured error is different from the true error by more than $\epsilon$ is less than $2e^{-2n\epsilon^2}$. Note that the crucial point here is that the test data was chosen randomly from the domain space.