It's just for slowing people down. "Cryptanalysis is an Electronic Warfare + Decrypt (encryption rating x 2, 1 Combat Turn) Extended Test," so that Joe Hacker can indeed do it in under a minute, but what can Joe Runner do during that minute?
Also, they have to decrypt every file/node/etc. individually, and you can always databomb things; they'll have to find and defuse those, too. Again, it's about slowing them down while you work.
This is the same as locks in SR; you can pick/hack/spoof your way through basically everything (biometrics are harder), and it doesn't even take very long. But, time is precious.
If you want Decryption to take longer, use Dramatic or Strong Encryption, or change the threshold to x2.5, x3, or even more.