Yes, depending on what they do. If they potter round the surface then no, not really, if they burrow into it, then locally round their holes, yes. I'd still doubt they do much to aid bulk flo' thro', but I haven't looked at that much. You'd need some real dynamic numbers then on how many worms per cm3, how far they burrowed and so on. Incidentally I bet there is pretty poor diffusive flow thro' silt beds.
More to the point tho' we're talking deep sand beds here, not deep silt beds. I don't think many people would have the patience to try and tweak tune a silt bed i nthe same way as a sand bed. However people do use silt beds, it's called miracle mud . There the macroalgae is the source of export, but the fine grain size and limited flow means there is ammonium reduced from nitrate at a very shallow depth and made available to the algae (optimising take up). But that's a whole new discussion