I did mine out at the lake last year. Took way too much time and effort, because it's difficult to prepare much ahead of time. My opinion:
1. Through bolting is the most solid and secure method. It's also a PITA and doubles the amount of work you have to do out at the lake.
2. Through bolted bunks are a PITA to remove once the wood gets old and starts rotting. As JRW160 noted, removing them is difficult because the head just rotates. Unfortunately, the previous bunks didn't have the heads embedded in 5200.
Next Time, I'm going to carpet all the bunks at home in the garage - it's a nice afternoon winter job. Then, I'll take the boat to the lake, dump it in, spend an hour cursing and getting the old carriage bolts out of the old bunk boards, put the new ones on and spend about 20 minutes lag bolting them in and be done. 5 or 10 years later when the lag bolts get loose, I'll just rinse and repeat. The problem with lag bolts isn't that the wood gets soft and the bunks come loose - it's that the wood gets soft and the owner chooses to live with it for too long and the bunks come loose. Make the decision to deal with it when you notice it loose, and life will be just fine.
1998 Maristar 200VRS