Laminitis is "just" an inflammation of the laminae so any place that bacteria can get in heightens the risk. WLD is a form of laminitis, or a precursor to, for example. So laminitis can result from either the lack of trim and/or the nails remaining. The nails will, IMO, cause a problem because without the depth of the shoe they will not be secure and their movement will damage the hoof more and more. Nails can be quite close to and can even cross through the laminae. With the combined stress of the walls pulling outward the nails moving, there will be more access points for dirt and bacteria.
Alwaysbehind brings up a valid point. I have actually never seen a nail stay in and the shoe come off. I took in a girl who threw one shoe in the trailer on the way here and another while waiting for us to get organized. Neither one left nails behind. But, of course, left the holes -- for garbage to get into.