What are cache.db-shm and -wal files?

I also first noticed them after updating to 10.8.3. They were most definitely not there prior to this release. I am also wondering why there are now three types of cache files, since no one has yet answered the question.

I am keen on regularly clearing my Safari cache

Which merely serves to make Safari slower.

Is this a new file system with the Safari update yesterday?

No.

Do I have anything to be worried about?

Only the fact that you're slowing down Safari by unnecessarily emptying the cache.

Write-Ahead Logging

They've been there. You didn't notice them before. This is normal system behavior. Grubbing around in cache directories is a waste of time.