Ok - what's silly about it is, we have better security in the 21st century. I have to show a valid ID badge to get into work and that is not a top secret spy base. We can monitor mobile phone calls now -albeit civil liberties prevent authorities doing this as standard. Does anybody think that a top secret base close to instigating a war with the Klingon Empire would NOT be monitoring local traffic? Why would it? FOR EXACTLY THE REASONS WE SAW IN THE MOVIE!
And Scotty doesn't flee - he sneaks onto a top secret spaceship with poorly trained security. In our office, if you see someone without ID, you are supposed to challenge them and that is everybody, not just trained security staff, who would immediately escort said unknown persons off the premises (or more likely to the brig on a starship). Standard security protocol should be to report in straight away as well let alone listen to what was being said on the communicator, asking intruder to pass you the communicator, or stunning prisoner and picking up communicator yourself.
Having no method of detecting incoming transporter signals is ludicrous. Transporter tech has been around for decades. I don't believe that nobody has thought of this as a security problem. Shields impliedly cannot be used all the time (otherwise why don't they?) so ships are incredibly vulnerable. We saw in WWII that science keeps pace with the technology (although some nations get an advantage by getting there first). Ships may have methods to try and disguise where on the ship the transport ends up e.g. by emitting an energy pulse to overwhelm sensors temporarily - so the ship knows that someone has probably been transported but they would not know exactly where but no detection at all is daft.
Narada was a civilian ship - with massively powerful shields, massively powerful weapons, and a lot of them, but inefficient sensors... and in a nation where intruders beamed in off a cloaked ship are a very, very real threat. I don't buy it as anything other than a plot contrivance. It's just silly.