First, a minor notational point: The ordinal in question is normally denoted $\omega_1^\mathrm{CK},$ with a subscript $1,$ not just $\omega^\mathrm{CK}.$ (It's Church and Kleene's effective analogue to $\omega_1,$ the first uncountable ordinal, not an analogue to $\omega.)$
As to the actual question, an ordinal $\alpha$ is said to be computable (or recursive) if there is a computable subset of $\omega\times\omega$ which, as a relation, is a well-ordering of $\omega$ of order type $\alpha.$
(By the way, this is a robust notion, in that you can look at recursively enumerable subsets of $\omega\times\omega,$ or arithmetically definable subsets, or even hyperarithmetically definable subsets, and you'll get exactly the same computable ordinals.)
Every computable ordinal is clearly a countable ordinal, since it is the order type of a well-ordering of $\omega.$
There are only countable many computable subsets of $\omega\times\omega,$ so there are only countably many computable ordinals.
So there are ordinals that are not computable, and the least such ordinal must be countable. That least non-computable ordinal is called $\omega_1^\mathrm{CK}.$
It's easy to see that if $\alpha$ is a computable ordinal and $\beta<\alpha,$ then $\beta$ is also computable.
It follows that the computable ordinals are precisely the ordinals that are less than $\omega_1^\mathrm{CK}.$
Of course, as suggested in the question, you can give $\omega_1^\mathrm{CK}$ a name (for example, "$\omega_1^\mathrm{CK}$") and "represent" it in the sense that it now has a name. But that doesn't give us a recursive representation of an actual ordering of order type $\omega_1^\mathrm{CK}.$
What happens if we take recursive representations of all the smaller ordinals (all those smaller ordinals are computable, after all) and piece them together? It turns out that there is no computable way to do this, so we can't get a computable well-ordering in this fashion. And this makes sense, since, by definition, the ordinal $\omega_1^\mathrm{CK}$ is not computable.
A second way of looking at this is via notations for computable ordinals.
Define what it means for a natural number to represent a computable ordinal by induction, as follows:
• The natural number $0$ represents the ordinal $0.$
• If $n$ represents $\alpha,$ then $2^n$ represents $\alpha+1.$
• If $\varphi_e$ happens to be a total recursive function such that $\varphi_e(0), \varphi_e(1), \varphi_e(2), \dots$ represent computable ordinals $\alpha_0, \alpha_1, \alpha_2, \dots,$ then $3^e$ represents $\sup_{n<\omega}\alpha_n.$ (Here $\varphi_e$ represents the $e^\mathrm{th}$ partial recursive function in some standard ordering.)
(This is a bit of a simplification. You'd actually define the natural ordering of these representations as part of the same induction, so you can require that $\alpha_0<\alpha_1<\alpha_2<\dots.$ By the way, if you read this in the literature, usually $3\cdot 5^e$ is used instead of $3^e,$ but this is just a historical accident that doesn't matter for anything. Also, just to be clear, although this is a definition by induction, it can't be formulated in Peano arithmetic. You can do it in ZF, of course.)
The set of all numbers that represent some countable ordinal is called Kleene's $\scr O.$ The natural ordering of these representations is called $<_\scr O.$
Every countable ordinal has a representation in $\scr O,$ and every computable ordinal greater than or equal to $\omega$ has infinitely many representations in $\scr O.$
You can see that $\langle \scr O, <_\scr O\rangle$ is a tree of height $\omega_1^\mathrm{CK}.$
But we can't use this ordering to get a recursive ordering of order type $\omega_1^\mathrm{CK}$ (for example, by finding a recursive branch through the ordering), since $\scr O$ isn't recursive. (It's not even arithmetically definable; $\scr O$ is a complete $\Pi^1_1$ set.)
For completeness, I'll mention that there's a third way of looking at all this: $\omega_1^\mathrm{CK}$ is the least ordinal $\alpha$ such that $L_\alpha$ (in Gödel's constructible hierarchy) is a model of Kripke-Platek set theory (which is like ZF but with separation and collection axioms limited to bounded formulas, and without the power set axiom).
This shows that $\omega_1^\mathrm{CK}$ is a very natural closure ordinal.
As for the last question — we're better than many theories. For example, $\epsilon_0$ is a computable ordinal, and we can write down a recursive definition of a well-ordering of $\omega$ of order type $\epsilon_0.$ But Peano arithmetic can't prove this is a well-ordering.
So this is an example of something that we know is true but that PA can't prove (the fact that the recursive ordering in question is a well-ordering).
When you go up to more powerful theories (for example, ZFC with large cardinals), we don't even know whether these theories are consistent, and, if they are, whether they actually have well-founded models. So who is correct – the theory ZFC + “there exists a ‘super-duper’ cardinal”, or the person who says “I don’t believe that ‘super-duper’ cardinals exist”? We just don’t know.
As far as I'm aware, the proof-theoretic ordinals of ZFC or more powerful theories haven't been extensively studied; it doesn't seem that there's a whole lot one can say about them (except that they're very complicated countable ordinals, much larger than $\epsilon_0.)$