Your situation is one where your repository is a Superproject importing several submodules. Some of which are Superprojects themselves.
You have complete control over your superproject, but cannot modify the external resources you import. However, you have complete access to all the submodules and nested submodules (otherwise you wouldn't be able to clone).
It appears that some of the resources you import from one of the Super-submodules are not needed in your project, and you'd like to get rid of them.
Recreate the external resource
Add as submodules only those submodules you actually need, instead of the Super-submodule that is creating fuzz. You'll have to modify the architecture of the project a bit to make the necessary modifications, but you'll manage in the end.
Exclude some submodules from cloning
As pointed out by phd, you may exclude some submodules from cloning. Some comments point out that you might even be able to prevent a submodule submodule from being cloned:
git -c submodule."third-party/submodule".update=none submodule update --init --recursive
^ a submodule of a submodule