I could be mistaken, but I think there is a difference between the 'deep litter method', which assumes a dirt floor and decomposition of litter, and simply having deep litter on a wood floor. On a wood floor, the litter must be kept DRY or the floor will rot. The litter needs to be regularly ( daily perhaps ) turned over right down to the wood. No decomposition takes place. If one has a dirt floor, fresh litter is added on top of whats down already, and the underlayer decomposes, which creates ( some ) heat and wonderful compost.
If the litter on a wood floor smells, its either wet ( and there can be lots of reasons for that ), or the coop is closed up too tight... in my opinion, after many many years with dogs, horses, stables and kennels. : )
I am presently using a couple inches of sand covered with several inches of shavings in my wood floored coops, and am finding it the best of both worlds. Dry dry dry.