I through bolt them like that so they will last longer....most of the bunks that i see fail is due to the lag bolts....it usually rots around the lag bolt easily then the lag bolt falls out....I countersink the heads obviously so they dont gouge the bottom of the hull.
also, i coat the wood with an outdoor sealer....something like what you would coat a wood deck....i figure if you can get the wood to resist absorbing any of the water, it will give it some extra life.
I dont bother using any glue to bond the carpet to the wood....i just use a staple gun on the seems which is on the underside of the bunk...and on the ends.
The carpet I used on these bunks was a real pain in the ass to deal with....as you can see, the edges are all fraid...the carpet strands would run just like a knit sweater. I still need to clean up the edges.