Because the text of the weapon:
QuoteIf this attack hits, the defender suffers 1 Critical Hit damage and gains 1 deplete and 1 jam token. Then cancel all Hit / Critical Hit results.
And the definition of "suffers" damage in the rules reference states:
QuoteIf an effect instructs a player to deal a damage card to a ship, this is different from the ship suffering damage. The card is dealt to the ship regardless of whether the ship has any <shield icon> (active shields).
My take is that if the defender still has shields the only effect (besides the two tokens) is losing one shield, not an automatic crit. Does that compute?