avast can't scan files that are password protected, it doesn't know the password.
There are many legitimate reasons why a file was password protected. For instance, the ones you're talking about. Lavasoft stores its data in a password-protected ZIP archives (to prevent other similar tools from messing up with them). It's really nothing to worry about - it's normal.
In AdAware and S&D, when you fix/remove things it keeps backup/recovery information so you can restore anything that was mistakenly fixed/removed, etc. After a reasonable time your system has suffered no adverse effects, you can get rid of the older recovery/backup points.
This should reduce the number of protected files.
