Ok. Let's go through this again. This is an apparent mission specific issue. In "The Darkness and the Light," where I am specifically ordered not to engage the Taranis, and it blows up a Hammer of Light ship I was supposed to disarm and disable, I am perfectly able to use subsystem targeting. It is only in the next mission, "First Strike," in which I am unable to target the subsystems of the Taranis. Thus far, "First Strike" is the only mission in which I have not been able to target subsystems on a capship.
As to your argument that the Stiletto does not need a target lock to destroy subsystems, this is only partially true. It does not require an aspect lock on a target. However, in order to destroy a particular subsystem in a timely manner, I must be able to at least have a basic radar lock on that system so that the missile initially targets it.