I've not had a problem - although you are correct in that I've observed the fighting conch digging in (usualy I see him after the fact) to the DSB. He usually only covers the lower half of his shell and doesn't do this in the shoal grass stand. There was a section of root/runner that was never buried and it's been further uprooted by their movements. However, plant health has not been negatively effected as the stand of shoal grass has increased plant count exponentially. I started with ~25 plants on 3 runners 3/26/06 and now, honestly, I can't count them all... my best guess after loosing count over and over is ~200 plants (and I'm being conservative).
The larger problem with the conchs (all) is that they tend to push their way through the seagrass stand. If shoal grass is your intended species, I would go with a smaller/ more nimble critter. I've kept mine because they are going into my upcoming seagrass tank which will be Thalassia dominant... they do great with thalassia. It's not that they are damaging the shoal grass, just that it doesn't look as "grassy" when it's all pushed flat. It may be helping the plant spread, but I can't tell for sure as it's spreading rapidly on all sides of the stand.
Hermits and snails are still your best bet. Conchs get large quick if food is plentiful.
Best of luck,
John.