That wouldn't be the case in many scenarios I can think of:

1. DB backup is compromised (from an offsite backup storage, think S3).

2. Developer laptop lost, with a copy of the database locally. (source code may be available, but the site-specific key probably wouldn't be. As that's a config var on the server).

3. SQLi that dumps hashes to the page.

I'm a big fan of making the job harder for attackers. There are lots of attack vectors where a 'pepper' value would be useless. But not all of them. And it's nearly free to implement. Might as well.