Silicon dioxide is used as an abrasive because of its regular crystaline structure- silicon dioxide or silica is sand, hence the name sandpaper. Because of its crystalline structure, its relatively inert nature, and the fact that it is polar (and so won't repel other polar or charged compounds), silica doesn’t contaminate surfaces except as dust- it does not readily adhere and interfere with subsequent coatings.
“Silicone” on the other hand, is a very different beast. It is derived from silica- through smelting with carbon, silicon dioxide (sand) is reduced to elemental silica and carbon dioxide. Elemental silica is then chemically converted into any number of silane products through combination with organic (carbohydrate-based) chemicals such as methyl chloride. These silane polymers possess properties that are very different from silica. Silicones are silicon-based polymers that are hydrophobic, which means that they do not like to interact well with water. Because silicones are long-backbone polymers with un-charged methyl side chains, they exhibit little interaction with uncharged and non-polar molecules. This means they exhibit very low surface tension. Thus, they have important functions as water repellents, antifouling agents, mold releasers, etc. (think Rain-X).
Silane-based products have a wide variety of important uses, and they are not to be terribly feared. A few molecules floating around a shop will not kill the possibility of finish coats adhering well. But treating a surface with such products prior to finishing certainly will. That said, the large size of polymeric silane molecules should prevent them from migrating into the surface of a finish, so even materials treated with these products should be renewable to accept finish coatings simply through a thorough and complete sanding.
Which brings us to sandpapers… For effective coating of surfaces, polymeric silane products like Rain-X are generally provided as molecular suspensions. Their use in sandpapers should not contaminate a surface because they are bonded in place on the sandpaper. And there is a logical marketing-based reason not to fear your sandpaper. Because sandpapers are used to prepare surfaces for finishing, a manufacturer would be committing suicide by treating their products with a transferable form of silicone.