I think that it is safe to say that the Enterprise's security is what tvtropes (WARNING: highly addictive website!) refers to as the Worf Effect, amusingly enough. It seems to get hacked every few episodes and they make a big deal about it being so tough- but if it's all that tough, how does it keep getting hacked? Data does it, the Borg do it, loads of aliens manage it both in person and remotely. Heck, Moriarty does it in part.
And when you examine much of the security, there are a lot of questions one has to ask. What sort of security is it to have someone recite a password out loud?
So, yea, it's supposed to be very difficult in theory so that they can show what a powerful enemy they are facing. Because if they weren't powerful, they wouldn't be able to hack the ship.
Edit: thinking about this a little bit further, you can make a few arguments for the reasonableness of these measures. Requiring a password while already within a system for every little thing is both obnoxiously annoying and likely to be deadly in emergency situations where split second timing is required.
For example, imagine a case where the Picard Maneuver needs to be done:
"Computer. Execute Picard Manueuver 117."
"Please state 32 digit security code to continue."
"I thought you said J117Z52Ketc. Was that correct?"
"I'm sorry. Let's try again. Please state..."
In addition, with how socially advanced the Federation is, the code is probably more in place to discourage anyone from accidentally doing anything. For example, you don't want the ship being navigated by the kids on board.
Finally, it should be noted that the Enterprise is the flagship, and therefore meets strange new life forms and new civilizations. Federation vessels which mostly just patrol Federation territory won't require security more elaborate than this on a day to day basis. One would suspect that therefore, since it is good enough day to day for the other ships, the security should be good enough for the Enterprise, or at least that's perhaps how the argument goes.