While I agree (mostly) with what you say, you have to keep in mind that no system is infallible. Even with quantum encryption, if someone wants to break the code, they will. It could take them days, months, years, but they will, at some point, break it.
But let's get back on topic, this is about intercepting stuff and not knowing what they say.
Like you said, laser transmissions are hard to intercept (if not impossible) without breaking the transmission. I don't know about sub-space transmission or Neko-like telepathy, since i don't know how they works, but pretty much anything else (electromagnetic signals) would be easily intercepted by a small scout ship, or a probe, with the proper equipment.