To bluntly answer the question: "Why not enable it by default?" The obvious answer is "because it has drawbacks". Otherwise it would be enabled by default :).

Looking at this article from Canon directly explaining the option for the 1DMkIII and 1DSMkIII, then at this one for the 7D, I think we can safely say that the effect will vary depending on the camera you have.

One thing that seems to remain constant between the 1D and 7D, though:

• Only works in Live View. And everybody knows that at the moment, Canon's DSLRs really suck at LiveView AF. It just lags too much. Even the most recent generations (Hybrid AF, from the EOS-M onwards) are still noticeably slower to achieve focus than when using the optical viewfinder.

The different types of Silent Mode I've seen so far while researching the subject.

1. Everything is slowed down. Mirror movement and everything. If that's the case, I suppose it increases the shutter lag, and maybe will limit your shutter speed?
2. Mirror stays up all the time. So you don't get the "clack clack clack" of the mirror in between shots.
3. Part of the noise is only delayed until you release the shutter button. Still called Silent because it allows you to put the camera away before releasing the shutter button, and muffle the sound if you need.

EDIT: Looks like the 5D Mk III's silent mode doesn't require live view, and provides modes 1. and 3. above. The 1D X also has silent modes in PDAF as well as Live View. The 1D mkIV, 1D mkIII, and 1Ds mkIII have a silent mode in PDAF but none using Live View.