I think one of the reasons is that Lean's approximation of defeq still works well enough in practice. As mentioned by others, you never really run into the kind of counter examples that break theoretical properties, but instead into examples where checking defeq is inacceptably slow, which remains an issue even when defeq is decidable.

From my understanding CiC is used because it allows using a unified language for proofs, specifications, programs and types, which greatly simplifies the system. For example, in Lean 4, more or less the entire system is built on the same core term language: Proofs, propositions / specifications, programs, tactics (i.e. meta programs), the output of tactics and even Lean 4 itself are all written in that same language, even if they don't always use the same method of computation. In my eyes, for the purposes of writing and checking proofs, CiC is quite complex; but if you want to capture all of the above and have them all checked by the same kernel, CiC seems like a fairly minimal metatheory to do so, even with undecidable type checking.