In over 25 cruises, I've never seen anyone questioned or detained because of prescriptions. I cruised before and after major knee surgery earlier this year and had several painkillers and antibiotics with me. I kept one "set" of pills for the number of days in one bag and another "set" in a different bag -just in case one got lost or fell in the water. One set had original bottles, the other set in a 7 day pill box.
I don't think the average cruise passenger fits the profile of a serial drug smuggler. I may be naive (don't think so), but I wouldn't worry about anyone questioning any prescription medications.