Sharpie markers are solvent based. Solvent-based inks should not be used on archival paper since it will soak through and damage the paper over time. There are no guidelines for what products are archival safe, but it is important to note that archival documents can be damaged by solvents.
According to the Sharpie FAQS, Sharpies may be used on CDs and solid, nonporous surfaces. Sharpies may be used on boxes and materials that are not to be preserved. Sharpies are not recommended for letter writing or cloth, since they are solvent based.
There is no information as to whether Sharpies deteriorate materials, but limited use is recommended since they are solvent based. Many artists use Sharpies for artwork without knowing how long the work will last; using them for scrapbooking and art is at your own risk.