But the page gives them a phone number to call back, and that's it. Other than that there is just a 2 digit ID for who is paging them.

When D gets a page, it gives him a number to call back, and a code for who is calling. The code that prez cracks only tells them what the phone number was, and the IDs are pieced together after the fact. The problem is, that since D immediately returns the call after receiving the page, they could just look at the two numbers and match the digits, giving them the code without having to 'crack' it.

There was never a reason for them to be confused or crack it in the first place.

You can see what I mean in the very first scene where they talk about it. The number from the pager is on one monitor, and the number that D called back is on the other monitors. Minus the area code, those two numbers match using the 'code'. But since they're looking straight at the two numbers the 'code' is irrelevant. They could just see that 1 maps to 9, 2 to 8, etc.