Encryption should be more workable as a plot device than an actual game mechanic. I'd assume that breaking normal encryption would be a standard part of hacking, so that should be subsumed into the normal rolls. Just assume everything is encrypted to some degree, and the normal hacking rolls deal with that.
Serious encryption should be reserved for really secure items. The big paydata should be encrypted to such a degree, it'll take a lot of special work to decrypt it. But in order to do that in SR4, you have to resort to contrived plot devices, like in
On The Run.