The problem is effectively decidable, and we will describe an algorithm. By way of preparation, we need to mention the o-minimality of the real exponential field, and Wilkie's solution to Tarski's High School Algebra problem.
The real exponential field $\mathbb{R}_{exp}$ is the field of real numbers with an additional unary function $x\mapsto e^x$. Wilkie proved that $\mathbb{R}_{exp}$ is o-minimal, meaning that that every definable set of reals is a finite union of intervals.
Note that the function $x^x$ is definable in $\mathbb{R}_{exp}$. Indeed, $y=x^x$ if and only if
$$\exists u\,\,(x=e^u\wedge y=e^{ux}),$$
(using $x^x=e^{x\ln x}$). Since definable functions are closed under composition, all of the tower expressions in $\mathcal{E}$ are definable in $\mathbb{R}_{exp}$.
Now suppose two expressions $f,g\in\mathcal{E}$ define the same function on the natural numbers. Let $S$ be the set of positive real numbers $x$ for which $f(x)=g(x)$. Then $S$ is a definable subset of $R_{exp}$. Therefore $S$ is a finite union of intervals. Since $S$ contains every positive integer, it follows that $S$ contains some interval $(x_0,\infty)$.
But all of the functions defined by elements of $\mathcal{E}$ are analytic on $\mathbb{R}^+$. It follows immediately from
the principle of real analytic continuation (see e.g. Corollary 1.2.5 of A Primer of Real Analytic Functions by Krantz and Parks) that $f$ and $g$ define the same function on $\mathbb{R}^+$.
So we are reduced to solving the identity problem for $\mathcal{E}$ interpreted over the positive integers.
This brings us to Tarski's High School Algebra Problem and Wilkie's solution. Tarski wrote down a set of axioms for the equational theory of the structure $(\mathbb{N},\,+,\,\times,\,e,\,1)$, where $e$ is binary exponentiation. These so-called High School Axioms are the (positive) semiring axioms together with the rules of exponentiation
\begin{align*}
&x^1=x,\,\,1^x=x\\
&(xy)^z=x^zy^z\\
%%%%%%%%%%%%%%%%%% Following Exponent rule corrected
&x^{y+z}=x^yx^z\\
&(x^y)^z=x^{yz}.
\end{align*}
Tarski asked if the whole equational theory can be deduced from these. The answer is no. Wilkie found 'exotic' identities not deducible from the above, and he gave a computably enumerable set of identities from which the whole equational theory is indeed deducible.
Returning to identities for $\mathcal{E}$, we now have an algorithm. Given a possible identity, use Wilkie's axioms to look for it by listing all equations between elements of $\mathcal{E}$ that hold for all natural numbers. At the same time plug in integers $1,2,\ldots$ looking for a counterexample. One of these two processes will terminate after finitely many steps.
Wilkie's paper is available from CiteSeer here.
There is a Wikipedia article on Tarski's High School problem here.
It would be interesting to know if there is a nice analytic proof (avoiding Wilkie's theorem on the o-minimality of $\mathbb{R}_{exp}$) that the functions defined on $\mathbb{R}^+$ by the expressions in $\mathcal{E}$ are determined by their values on the positive integers.