First, the infamous eye-hand scene

But in Echoes its either scarred over or perhaps even has its own little tiny visor.

But her final form, where she’s absorbed enough power her outer armor has burned away, the eye is shown to be still under there.

Anyway, a friend of mine noticed in  Super Smash Bros Ultimate she holds her hand close to herself a lot of time. 

So I can’t help but think she hurt her eye alot by accident and it affected her muscle memory.

(Dark Samus keeps ending up more and more adorable the more I examine her and  like the Biolizard in Sonic Adventure 2 

I kinda wish

she got a different character arc/role. Ah well,  it was the days before things like Venom where fandom embraced monster characters.)