You could defeat this analysis by actually broadcasting noise on all frequencies, so the transmission frequency is indistinguishable, assuming the encryption used is also indistinguishable from a random oracle. But now you have a noisy point source in the sky, even if you can't decipher the contents of the message.
Succinctly put, obfuscation techniques like frequency hopping spread spectrum are tactical techniques that try to hide transmissions from actual radios in widespread use, not hide the existence of the radio signal in some physical sense. FHSS radio transmissions look like noise sources, not silence. Which is basically what SETI is looking for -- sources of radio noise unexplained by our understanding of astronomy.
GPS is not below the level of background noise. Not is sonar.
With frequency-hopping you still have spikes in the spectrum around the frequencies you hop between, but with most modern systems you no longer have anything distinctive to find.