Even the SE version still had Shaw, at least it did before 2004.
Anyway, I can sort of see how people might not immediately recognize the Shaw ghost as Anakin since the ghost form is healed and in Jedi robes. But that’s what’s cool about it. It requires the audience to turn a few cogs in their brains to figure it out: Obi-Wan was a Jedi and he died…now he’s a ghost. Yoda was a Jedi and he died…now he’s a ghost. So who is that 3rd guy with them? He must be a Jedi…oh, it’s Anakin, because he became good and died as a Jedi! Things don’t need to be so explicitly spelled out as to awkwardly paste Hayden’s head from episode 3 onto the scene, especially when the Hayden ghost fails on both a visual and thematic level.