No, charging the yo-yo's doesn't change where they hit the opponent. d-smash always hits opponents in the direction Ness is facing, u-smash always sends up. I'm using first and second hit to signify which side of Ness the yo-yos are on when I hit them, 2nd hit is the later part, the yo-yo is in front of Ness, sending forwards. This hit is better though its delay due the its disjoint, the low angle it hits people at, and the range. The first hit would bounce them off the stage, which may stage spike but also allows players to pick up on it and attempt ledge tech much easier.
Overall, I dont find myself using them too much, his other ground options, his OOS options and his DJC options more than often overshadow anything you would get using them.