There's an interesting situation here: while the question itself isn't a duplicate, a previous answer of mine I think resolves it. I don't quite know what to do in this case, so I've written a same-spirit, different-phrasing below, and not marked this question as a duplicate; to avoid "double-dipping" on reputation, I've marked my answer community wiki.
The difficulty here is that limit stages wind up more complicated than they look at first. The weasel words here are
its fundamental sequence.
The key point is, there is no unique fundamental sequence for a limit ordinal! The "$\lambda$th hyperfunction" isn't fully determined by $\lambda$; we also have to choose a fundamental sequence for $\lambda$ (and indeed for each limit ordinal $<\lambda$). One might hope that this choice winds up being insignificant, but in fact it's not: different hyperoperations corresponding to the same ordinal can vary wildly.
If you don't require canonicity, then there's no problem - fixing a system of fundamental sequences for all limit ordinals up to a certain point will define a hyperoperation at that point - but the point is that no good "all-the-way-up" (or even a-little-bit-of-the-way-up) theory of hyperoperations exists.
So what happens when we actually do talk about ordinal-indexed hyperoperations?
When we say something like "the $\omega^\omega$th hyperoperation" - e.g. in the context of fast-growing hierarchies - in the background we're assuming a fixed notation system for the ordinals in question, and this amounts to a choice of fundamental sequences. But this notation system can only reach a small ways up (e.g. to $\epsilon_0$ in the case of the Wainer hierarchy); in particular, there is no recursive way to assign a unique fundamental sequence to every recursive limit ordinal.
- This is reflected in the non-linear structure of Kleene's $\mathcal{O}$: Kleene provides a system to (essentially) assign fundamental sequences to recursive presentations of recursive ordinals, but two different presentations of the same ordinal can get different wildly fundamental sequences.
That said, there is a arguably-reasonable way one can try to go beyond $\omega_1^{CK}$ (indeed, all the way up to $\omega_1^L$, the first $L$-uncountable ordinal) in a canonical way - mastercodes. But this gets extremely technical. And it's consistent that $\omega_1^L$ itself is countable, so even this trick won't get us very far.