Here's a really crazy theory

Koishi's eyes have looked kinda weird since HM, haven't they? What if closing her third eye didn't just block her mind-reading ability, but also made her actually, physically blind?

I'm sure that's not the case, since she doesn't seem to have any trouble seeing the world around her, but the light in her eyes remind me of how some blind peoples' eyes can look

If it's intentional, then it's probably just meant to represent her psychic blindness, not a physical condition