Though Yugi was a foot shorter than Shadow and had to be on his tip toes to wrap his arms around her shoulders, he honestly didn't care. All he cared about was showing Shadow that she was not alone. That she had him too to help her and could come to him for anything, be if it was the most simplist of things such as talking to wanting to be in his company, even if it was to be Soul room. He would be fine with that. He also thought the Spirit, Yami to be part of their little misfit family, and when he got the chance, would tell him so and that he would be here for him as Yami has been for him and Shadow. 

Shadow having gone to sitting down and Yugi did feel a little more comfortable with hugging Shadow still, but took to notice her voice change and something that Yugi only continue to hug her, allowing her to let it out if she so wanted, not knowing how long it had been since she had such affection and or physical contact. "It's okay." He was glad to call her family.