I think you are right. Depending on how you look at it, this story "pages within books within encyclopedia within..." may actually be a better analogy with cardinals than with ordinals, although the two have a natural correspondence for exponentiations of $\omega$ / $\aleph_0$ to finite powers.
Ordinals are about enumerating things one after another, and it is perfectly fine to imagine first taking $\omega$ pages and assembling them into book $0,$ then taking another $\omega$ pages and assembling them into book $1,$ whose pages have numbers $\omega + n$ for $n\in \omega,$ and then taking the next $\omega$ pages and putting them into book $2$ which has page numbers $\omega\cdot 2 + n$ for $n\in \omega,$ and so on. Then when we're done assembling the encyclopedia with $\omega$ books, the $n$-th page in book $k$ has number $\omega\cdot k+n.$ Then we can start a new encyclopedia, whose $0$-th book has $0$-th page $\omega^2,$ first page $\omega^2+1$ and so on.
The thing to realize is that what we're doing here is enumerating off pages. The books and encyclopedias and so on were just conceptual devices to organize the layers. Something we'd call an ordinal notation more formally, and I've included the more standard version of the ordinal notation side by side. Something we should take note of on the long haul up to $\omega^\omega$ is that at no point are we more than finitely many layers deep in our categorization. Even if we're at the googolplex-th hyperlibrary or whatever we want to call it, it is a finite iteration of the original concept of the book. We just had to invent it at a certain point to continue our story once we had enumerated so many pages that they filled a whole $\omega$-sequence of googolplex-minus-one-th hyperlibraries.
As such, our pages before the $\omega^\omega$-th have numbers of the form $$\omega^n\cdot a_n+\omega^{n-1}\cdot a_{n-1}+\ldots +\omega\cdot a_1 + a_0$$ where the $a_i$ are natural numbers, so they each correspond to a finite sequence of natural numbers. It's a common exercise in introductions to cardinality to show that the set of all finite sequences of natural numbers has cardinality $\aleph_0.$
However, I think most people who would be told an abbreviated version of the story you lay out would have a much different picture of what the end state after $\omega$ iterations of "books within encyclopedias within..." would look like. One might imagine a whole completed infinite hierarchy, in which case it would make sense to ask simultaneously "which $n$-hyperlibrary is the page in" for all $n$ and there would be no reason to expect that all but a finite number of answers would be $0$.
The pages aren't enumerated up from the bottom, rather they come into existence all at once in this structure. So a page is characterized by an $\omega$-sequence of natural number coordinates, where the 0-th coordinate tells you the page within the book, the 1-st tells you the book within the encyclopedia, the googolplex-th tells you the googolplex-minus-one-th hyperlibrary within the googolplex-th hyperlibrary etc. And it's an equally standard exercise to show that the cardinality of the set of all $\omega$-sequences of naturals, i.e. $\aleph_0^{\aleph_0}$, comes out to $2^{\aleph_0}$ which is uncountable.
Note that in this picture, there is no way to order the pages bottom up like we did in the ordinal picture. The most obvious way to order them would be kind of the opposite: we look for the lowest level of the hierarchy (i.e. the smallest number coordinate) on which they differ and order them according to that. (So if one has a smaller page number within their book, it is smaller, even if the book it's in has a larger number.) This is not a well-ordering and thus doesn't really correspond to enumeration.
Also note that as I mentioned at the top, this irreconcilable divergence between the two pictures only happens when we get to infinite powers. The ordinals less than $\omega^3$ can be written $\omega^2\cdot l+ \omega\cdot m + n$ which is three natural number coordinates. The definition of $\aleph_0^3$ is the cardinality of the cartesian product $\omega\times\omega\times \omega,$ which is the set of all ordered triples $(l,m,n).$ Both are described by three natural number coordinates. While it's important to keep the concepts separate, since they do eventually diverge, this shows why whoever told you this story might have overlooked the potential confusion as to what story we're telling when we get to $\omega^\omega$ or $\aleph_0^{\aleph_0}.$
As to how to "reach" uncountably many pages, it was explained briefly in a comment and link by Don Thousand, and has probably been explained more thoroughly elsewhere on this site but I'll try to elaborate. As we enumerate, the organizational story we tell ourselves inevitably runs out. We can go substantially higher than $\omega^\omega$ just by continuing to iterate after that, but words and symbols are only countably infinite in number and they eventually must fail us.
In the absence of a full story for how we count to an uncountable number, we fall back on some more abstract arguments. The ordinals that we can enumerate up to explicitly in a fashion like we were doing above correspond to computable well-orderings of $\mathbb N$ (these are called recursive ordinals). However, there are many more well-orderings of $\mathbb N$ than that. We know this since when we arrange the recursive well-orderings in order of how high they go, they form a countable well-ordered set (there are countably many recursive relations after all) so they correspond to a well-ordering of $\mathbb N,$ which by its definition goes higher than any recursive ordinal. We call arbitrary well orderings of $\mathbb N$ countable ordinals.
Now we can repeat the same argument with all of the well-orderings of $\mathbb N,$ not just the recursive ones. Arrange them in order of how high they go and the result is a well-ordered set which by its definition goes higher than any countable ordinal. This is the first uncountable ordinal.
So while we can enumerate an uncountable number of pages in a sense (and I'll note that obviously this can be made much more rigorous than I'm probably making it sound, using axioms of set theory and all of that), it is not nearly as constructive a process as for small countable ordinals like $\omega^\omega$ or even much larger recursive ordinals, and it's not visualizable in any useful way I'm familiar with. (But a point in favor of its 'constructiveness': the argument does not use the axiom of choice.)