The details may vary according to the syntactical specifications of the language but, in general, nothing forbid to have $\exists y A(x)$ when $y$ is not free in $A(x)$; the usual recursive definition of formula in FOL is :
(i) if $t_1,\ldots,t_n$ are terms and $P^n$ is an $n$-ary predicate symbol, then $t_1=t_2$ and $P^n(t_1,\ldots,t_n)$ are atomic formulae;
(ii) if $\varphi$ is a formula, then $\lnot \varphi$ is a formula;
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(iv) if $\varphi$ is a formula, then $\forall x \varphi$ and $\exists x \varphi$ are formulae.
Intuitively, if $y$ is not free in $\alpha$, then $\forall y \alpha$ and $\exists y \alpha$ have the "same meaning" of $\alpha$.
We can prove it "formally" showing that :
if $y$ is not free in $\alpha$, then $\vDash \alpha \leftrightarrow \forall y \alpha$,
i.e. $\alpha$ and $\forall y \alpha$ are logically equivalent, and the same for $\exists y \alpha$.
We can apply the above result to : $∀x(∃y(A(x)))$ and we get that it is equivalent to : $∀x(A(x))$.
The semantical specifications for the quantifiers are [according to Herbert Enderton, A Mathematical Introduction to Logic (2nd - 2001)), page 83-84] :
We say that a structure $\mathcal A$ satisfy a formula $\varphi$ with an assignment function $s$, in symbols : $\mathcal A \vDash \varphi [s]$, when :
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$\mathcal A \vDash \forall x \varphi[s]$ iff for every $d \in |\mathcal A|$, we have $\mathcal A \vDash \varphi[s(x|d)]$
and :
$\mathcal A \vDash \exists x \varphi[s]$ iff for some $d \in |\mathcal A|$, we have $\mathcal A \vDash \varphi[s(x|d)]$.
Thus, consider a structure $\mathcal A$ and a function $s$ and apply the above definition; $\mathcal A$ satisfies $\forall x (\exists y A(x))$ with $s$ if
$\mathcal A \vDash \exists y A(x)[s(x|d)]$, for every $d \in |\mathcal A|$.
And this, in turn, means :
$\mathcal A \vDash A(x)[s(x|d)(y|e)]$, for every $d \in |\mathcal A|$ and some $e \in |\mathcal A|$.
But the variable $y$ does not occurr free in $A(x)$ and thus it does not matter what is the "denotation" that $s(x|d)$ assign to it. So we can discard $e$ and we have :
$\mathcal A \vDash A(x)[s(x|d)]$, for every $d \in |\mathcal A|$,
and this amounts to : $\mathcal A \vDash \forall x A(x)[s]$.