It depends on the packaging material and the application. For sensitive products that have a long shelf-life the packaging will likely be sanitized or sterilized. I've been a quality manager at an extended shelf-life dairy / beverage manufacturer and we sterilized our packaging just prior to filling done at the filler in a HEPA environment. This is also normal for aseptic filling processes as any bit of potential contamination on the package will affect the shelf-life severely during ambient storage.
The other process where sanitizing is used is caps in beverage applications. The capping equipment and process is generally not "as clean" as the filling equipment itself so many processes will sanitize their caps just prior to application with a sanitize chemical, ozone, or even UV.
MOST processes and facilities DO NOT sanitize or sterilize packaging.