It's a common misconception in games that collision boxes (the parts that "hit" and "are hit") match the character models, especially in fighting games where we expect our opponent to get hit if our sword crosses our opponent's foot. There is no way to know precisely where the hit- and hurt-boxes are until a viewer gets made in the distant future, but basically, although Lucina's sword is clearly crossing Pikachu's physical model, the part of the sword defined internally to the game as "this hits stuff" is not intersecting the part of Pikachu defined as "hittable." Most likely, Pikachu's hittable area has pulled back farther than his in-game model has, since Lucina's sword usually attacks in a reliably sword-swing-ish shape.
You can see Nintendo fiddling with this in every update; there's always a few changes that are something like, "changed hittable area to better match animation" or something, like how they made Ike's Fair and Jab(3) vertically larger to match where his sword is, whereas before the change, the extremes of his swordy-swingy-whoosh-thing (what I consider to be the visual cue for "this should hit") would go through opponents. All you can really do is take it to the lab (like you appear to have done) and figure out what's happening. I bet if you fudged Lucina a little closer, you'd probably register the hit.
