Mike,
If you can use the undersides of the bench tops, great; if not, I'm in the drive 'em in camp. With small-headed nails like brads you can easily drive them deep enough to never, ever be a problem.
"I recommend against sinking anything below the surface: you'll forget it, and it will be a land-mine at some point in the future (... deep chisel cut?)."
Work on your bench, not into it.