Let $p$ and $q$ be prime numbers and $\phi$ Euler's totient function. Is there an efficient way of computing $\phi(\phi(p\cdot q)) = \phi((p-1)(q-1))$, that is not simply based on factoring $p-1$ and $q-1$?
Obviously, if $p$ and $q$ do not equal two, $p-1$ and $q-1$ are even and consequently their prime factorization is entirely different from the prime factorization of $p$ and $q$. Therefore I assume that no such shortcut exists.
Do I overlook something?
No, not efficiently, not in general. Suppose $p=2p'+1$ and $q=2q'+1$ where $p',q'$ are prime. Then factoring $pq$ is believed to be hard. (Indeed, these primes are known as safe primes, and factoring a product of two safe primes is believed to be hard.) However we have
$$\varphi(\varphi(pq))=\varphi(4p'q')=2\varphi(p')\varphi(q')=2(p'-1)(q'-1).$$
If you could compute $\varphi(\varphi(pq))$ from $pq$ efficiently for $p,q$ of this form, then you could factor $pq$ efficiently for $p,q$ of this form. The reduction works as follows. Consider the quadratic function $f$ given by
$$f(x)=(x-p')(x-q')=x^2 -(p'+q') + p'q'.$$
We can compute the coefficients of $f$, as
$$p'+q'=[pq-2\varphi(\varphi(pq))+3]/4$$ $$p'q'=[pq+2\varphi(\varphi(pq))-5]/8$$
so you can use the quadratic formula to solve for the roots of $f$ and recover $p',q'$. From this the factorization of $pq$ can be recovered.
So, no, you are not overlooking anything. There is likely no efficient way to compute $\varphi(\varphi(pq))$ for arbitrary numbers $pq$ (unless factoring is easy).
