While it is difficult to provide one general answer to your question, if I had to limit my response to one word, “yes”, because the cost of parts is typically very dependent upon the cost of the raw materials, and the cost of raw silicone is usually more expensive than the cost of plastic resins. Even the least expensive silicones may cost $5 – $10 per pound, while plastic resins run closer to a couple dollars.
However, in the medical device market, lots of parts are very small or microscopic. Micro molding is much less dependent upon the cost of the materials since there is so little physical volume. The cost of a micro part is driven more by the processing that goes into demolding, quality control inspection, and packaging, as all of these activities will require the use of microscopes that would not be required for larger parts.
But in general, molded or extruded silicone medical parts will cost more than plastics, thermoplastic elastomers, and petroleum based rubbers. The tradeoff is the biocompatibility and implantability that you get with silicone products, as well as other contributing factors like the physical, chemical and mechanical properties required of the device. Silicone may not always be the best material for the job, but when it comes to soft, flexible parts for medical applications it is a very good place to start.