I am not sure why things are getting uninstalled. I have read where players regardless of how their game is installed will see things missing. I've even had store items go missing as well. So it's not just you.
I've actually deleted all of the cache files, log files and tag file in the Sims 3 folder before as part of a test. Leaving Options.ini because I don't want to loose my graphics settings and gameplay options. All still loaded just fine.
However, there has been a few times where I've deleted all the files in the DCBackup folder except for the ccmerged.package file and have lost installed items. Due to that I leave those files alone. It doesn't hurt anything leaving the files there and prevents having to reinstall what goes missing, at least in my experience.
To me it seems more like personal preference to delete the files in DCBackup or not. I am not entirely sure if that will fully fix the issue, but it might be worth a try.