Currently seccomp is unconditionally turned off.
Note that cgroups are also unconditionally off, which may not be desirable.
libclsync has no seccomp or cgroups relate code. These use flags belong to the main clsync code, see app-admin/clsync. Both packages came from the same code, but libclsync is a supplement, so its package have control via USE flags only for those options which affect real code.