It's a very useful convention, at very least; in some cases, though, it really is the correct value given the definitions involved.
As you note, the intersection of an empty collection of sets it's not empty; rather, it's everything. This can be seen by expanding the definition. Suppose $\mathcal{A}$ is empty. Then
$$\begin{align}
x \in \bigcap \mathcal{A} &\iff \forall A\,(A\in\mathcal{A} \to x\in A) \\
&\iff \forall A\,(A\in\emptyset \to x\in A) \\
&\iff \forall A\,(\mathsf{False} \to x\in A) \\
&\iff \forall A\,(\mathsf{True}) \\
&\iff \mathsf{True}
\end{align}$$
So every $x$ is, in theory, a member of the intersection. This isn't a set, unless implicitly all $A\in \mathcal{A}$ are subsets of some set $X$, as is typical. *When that's the case, the empty intersection is $X$, because then implicitly $x$ is constrained to be in $X$.
A similar situation arises more generally in complete lattices — partially ordered sets $(X,\preceq)$ such that every $Y\subseteq X$ has a $\sup$ (least upper bound) and an $\inf$ (greatest lower bound) with respect to the ordering $\preceq$. Work through the definitions and you'll see that in a complete lattice,
$$\begin{align}
\sup \emptyset &= \mathbf{0} \quad\text{the 'bottom', least element, and} \\
\inf \emptyset &= \mathbf{1} \quad\text{the 'top', greatest element.}
\end{align}$$
In fact, because the definition of a complete lattice implies that $\sup$ and $\inf$ exist for $\emptyset$, the definitions of $\sup$ and $\inf$ imply that for every element $x$ of the lattice, $\sup\emptyset \preceq x \preceq \inf \emptyset$, and this establishes that a complete lattice actually has least and greatest elements ($\mathbf{0}, \mathbf{1}$ respectively).
This is consistent with what happens with $\bigcup$ and $\bigcap$: these are $\sup$ and $\inf$ operations in powersets $\mathcal{P}(X)$, which are complete lattices with respect to the partial ordering $\subseteq$.