Allyfish, I have personally never seen any fasteners other than lag bolts holding flat bunks to the brackets on a bass boat trailer. I have seen carriage bolts on older big boat trailers.
Something else to consider when a few of you were talking about only three bolts holding the vertical bunks is that there is a compression factor also, as with any bolt on situation.
That is odd that your bunks have rot already, I have several Allison's in my area in the mid 90's on up that have never had the bunks replaced and are still solid.
Those older bunks probably wouldn't get past the EPA now days though.
The vertical bunks are under the strakes where the main stringers run inside the boat. There is no problem with the full weight of the boat resting on just the two bunks.
There was also mention of having to pick up the bow when loading at times because the bunks were too low, (Gotmyally) that is not the case at all. That issue comes from the trailer being backed into the water too deep. The front roller and guide bunks raise the bow over the bow stop when the trailer is in the correct depth.
Just a few thoughts.