To be fair, nothing that they use in Discovery are superweapons and all of their tech can easily be put forward as spy stuff. We’ve also seen that Section 31 is directly involved with various classified projects to begin with, which is why they were posted on Discovery in Episode 3. Moreover, DS9 explicitly says that Section 31 was operating since the start of Starfleet but that they had almost no oversight for 200 years. They weren’t merely intelligence operators. They were active assassins who are comparable (and were directly influenced by) the CIA. They were made to take care of any and all threats to the Federation that couldn’t be taken care of within the normal scope of things. Is it really so unbelievable that this secretive black books organization has spy tech that’s unavailable and unknown to most of the populous? I mean… we do that today with various intelligence and military agencies.