Shrink is a common issue in all injection molding processes, both silicone and plastic. As long as you are working with a skilled manufacturer, who has ample knowledge in material science, they should know how to account for the shrink in your design. Silicone shrinks more predictably than plastic, so it is easier to account for. All plastic resins have different shrink rates, and they are much larger than the shrink rates of silicone. Plastic shrink can also result in sink, which can be a large problem atheistically.
Shrink is always accounted for in mold design. The manufacturer increases the cavity to be 1-4% larger than the desired part, based on the material data sheets and the shrink rate. When the product cools or cures in the mold, it will begin shrinking. Shrinking will continue to happen to the part for the next 24 hours. If you are ever doing measurements on critical dimensions of a part, it should wait until 24 hours after molding.