No, I doubt that it can pierce Susano'o. For one, the sword was never described as being omnipotent or all powerful - all that was said was that anything which it
managed to pierce would be sealed into its Genjutsu. Not that it could pierce and seal
everything. It's a spiritual weapon, but it needs to turn physical to pierce its target. We saw it physically chop off the hydra's heads [
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] and deliver physical damage to Orochimaru when it pierced him [
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]. So I wouldn't back the logic of those saying; "Oh, it pierced Oro so it can pierce something as sturdy as Susano'o", since the blade lacks grand piercing feats.
You also need to wonder whether actual chakra (like Susano'o) can be put under a Genjutsu.