Most barnacles do not hurt sea turtles, as they are only attached to the shell or skin on the outside. Others though burrow into the skin of the host and might cause discomfort and provide an open target area for following infections.
Excessive barnacle cover can be a sign of general bad health of a turtle. Usually sea turtles are debilitated first, and then become covered in an extensive amount of other organisms, such as barnacles and algae.
Luckily turtles are very resilient and can sometimes recover from such infestations.
References:
Monroe R & Limpus CJ 1979. Barnacles on turtles in Queensland waters with descriptions of three new species. Memoires of the Queensland Museum 19: 197-223. Ross A & Frick MG 2007. From Hendrickson (1958) to Monroe & Limpus (1979) and Beyond: An Evaluation of the Turtle Barnacle Tubicinella cheloniae. Marine Turtle Newsletter 118: 2-5.