>In practice, people write their programs in a programming language. Some languages (e.g., C, Java, Lisp) only provide leaky abstractions, so programmers always have access to the internal representation of everything, to the detriment of modularity. But there are languages (e.g., Standard ML) that aren't hobbled in this way. ... writing a function that inspects the representation of an abstract type isn't “difficult” - it's literally impossible.
Alright, at that point it becomes an issue of "what kinds of things count as computations" for the purposes of the CTT. You're right that some languages simply lack certain capabilities, but that's an issue of access, not computation per se. You can get the same result in pure math:
"C is incapable of computing the zlobnorg of a matrix."
'Ridiculous! I'm sure I can write a program that does it! So, what exactly is a zlobnorg?'
"Sorry, only the matrix itself can answer that."
If you're going to go that route, then yeah the CTT is false -- likewise, TMs can't see inside black holes, so they can't "compute" that either.
But the "computations" referred to in the CTT are assumed to meet certain criteria, e.g. that there's some API exposed for accessing the relevant information, and the output is a "pure function" of that input (or at least makes any external state changes accessible, etc). But then once you've done so, all the Turing-complete languages can access said information information and compute the correct result.
Now, if your point is that the day-to-day work of a programmer is a lot more than writing pure functions: I whole-heartedly agree and have said the same thing myself. I cringe at the whole "Maxwell's equations of programming". Of course you have to care about external state and access privileges and race conditions and whether the API is usable, etc -- things that the CT notion of "computation" doesn't deal with. But, for the same reason, that's also orthogonal to the CTT.