Let's not forget that time when primitive 20th century freezer jockeys were thawed out on the Enterprise D and a sleazy 80s business man was able to do pretty much whatever he wanted with the computer. When Picard yells at him, he replies that if there were things he shouldn't be allowed to do, why didn't they set the computer to not allow it? And Picard replies that people shouldn't have to be told they aren't allowed to do certain things, they should be able behave without the computer forcing it.
So, the reason they have such a huge security issue is that they run everything on the honor system. Though I suppose this was right after Worf took over security, so I guess that makes sense.
The first time I saw that episode, I don't remember how old I was, but it was one of the first times I was left home alone. And by total coincidence, right when it was at the most intense part of the episode the power went out at my house. It was night time, during a thunderstorm, and no one else was home.
And then I had to brave the basement to check the breaker box. In the dark. Which was a little Home-Alone-evil-furnace-scene for me under normal circumstances.
The gang goes infiltrate some fancy pants Starfleet symposium -posing as captains because reasons- in order to find the infiltrator. But it turns out they're all infiltrators.
Section 31 actually knows about all the infiltrators, but at least in early stages of their infiltration when they're trying not to arouse suspicion they end up doing a better job than the human admirals would have anyway, so they're allowed to do their thing.
I mean, in fairness their strategy for space exploration seems to be to point a starship in a random direction, hit "go" and beam down to every planet with a remotely breathable atmosphere in their PJ onesies.
The impressive part is they still seem to be the dominant superpower in half the galaxy, so... yay for them.
I highly recommend the book Pandora's Star by Peter Hamilton. They explore using tiny wormholes. They move them, poke a powerful sensor suite though, scan, retract, and close, gradually moving in on prospective planets. They have powerful forcefield to protect against anything coming in the other way. Makes sense to me.
Being an admiral is great. You always have one free violating the prime directive or resisting a direct order from starfleet command and still be captain.
They had to keep things fair for the Romulans. It's not like cloaked ships have ever gone undetected by Starfleet vessels. They always see tachyons or someshit.