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.