_cos and _sin are underscored, and as such were never really "included" with Swift. They are vestigial implementation hooks that we can't really remove. The expectation is really that you get cos and sin either from the platform libc (as you show) or from Numerics, like the rest of the C math library.
However, it is somewhat troubling that LLVM is generating a call to a function that doesn't exist (or isn't linked) in your environment. If you have just a call to _cos (no matching _sin, and no Glibc import), does the linker find cos successfully?
OK, that's enough to tell us that this is just garden variety libm-not-being-linked-by-default-on-Linux, rather than LLVM doing something sneaky with sincos formation. If you use Numerics or the Glibc module, then libm will be linked for you. If you want to avoid using them, you'll have to ensure that it gets linked into your binary.
The best solution would be to use one of the modules that actually provides the feature, but if you really can't for some reason, then linking it manually ought to suffice.