So far as I am aware, with my somewhat limited spiral knights experience, every attack on the silent nightblade, be it charged, explosion, or normal swing, should be doing shadow damage.
Additionally, I'm led to believe through experience and the wiki that shadow damage deals extra damage to slimes and lichens, as noted by the higher and more tan/orange/bronze numbers produced.
Normal swings are doing extra damage. The explosions *after* a charged attack are doing extra damage. The charged attack swing itself, however, is showing normal damage numbers on the same mobs. Is this normal and expected? Is it resultant of a recent patch?
It's doing the actual shadow damage, it's just that normal damage numbers are showing.
It's one of the oldest glitches in the game.
Don't worry about that, it's doing the actual damage.
Even if it was the 'big' numbers, it'd be doing the exact same number, so it doesn't matter.