Yes. Simply put, file permissions can't change on their own accord, something needs to do it maliciously, or you've got a serious hardware problem. They simply can't change on their own accord.
You may see permission errors when doing a repair, but they're most likely all benign, such as a file being 664 when it was originally 644 or vice-versa. These are usually due to transient files being re-created after installation, when the running application has a different UMASK set to the one that initially created it. Certainly every error I've seen when running these repairs could be safely ignored as it was of this nature.
The repair permissions facility can only check permissions from software installed by PKG files (including anything installed via Software Update), as it simply extracts file details from the relevant BOM files, and changes permissions back to how they were when the relevant software was initially installed. It can't do anything with applications installed via other means, or with any of your own data files. So running to resolve issues with your own data files is obviously pointless.
Repairing permissions was necessary in the early days of Mac OS X when you could still boot up into Mac OS 9, as the latter OS didn't honour them properly. In particular some software installers than ran under Classic could be really problematic and mangle core operating system files. Since Mac OS 9 and Classic are no longer an issue, these problems can no longer occur.
So unless someone has been doing silly things in terminal with chmod, chown and chgrp, or there's a really badly behaved application, there's no point doing to unless you want to waste time.