By RAW, there is no indication that commlinks are exempt, so it would imply that yes the commlink does in fact cost double. Personally, I would say the commlink and commlink accessories would cost the multiple as by RAI (they don't really seem any different to the implant that customization or enhancements to cyberlimbs.
Of course, I would rule that it only applies to the hardware. Any software or programs shouldn't have the multiple applied.