##It helps him focus
It helps him focus
From a transcript of the film Captain America: Civil War
Tony Stark: Lordy! Can you even see in these?
Peter Parker: Yes. Yes, I can! I can. I can-I can see in those. Okay? It's just that... when whatever happened, happened... it's like my senses have been dialled to 11. There's way too much input, so... they just kinda help me focus.
Evidently, Peter has included them to help him see, and Tony has kept them because he realises he needs them even after the upgrade.
###Out-of-universe
Out-of-universe
Gives the character some expression and emotion and makes it more humanly and therefore easier to relate to.
