Having had 2 pontoons and 2 different trailers have had issues with carpeted wooden bunk boards on both, carpet tearing, boards rotting out within 2-3 years and screws pulling out bunks falling off you name it. I had been looking for different option for a few years and found a company that makes Poly bunk board that actually look like wood grain, they are quite spendy but after all the headaches wooden bunks gave me over the years these things are awesome, plus the pontoon loads and unloads a lot easier too. Here is a link to the product I have been using going on my second season. I highly recommend this to anyone who wants to upgrade the carpeted bunk boards.
http://www.ultimatebunkboards.com/index.html
http://www.ultimatebunkboards.com/index.html