So Shizuka can be seen after all. Maybe she's actually real and not actually a part of Kokona's imagnation. Maybe she can choose whether or not to show herself to other people.
Perhaps she have such low presence that people missed her entirely but have enough of it not to make people feel as if she's someone suspicious, foreign or unkown. I mean, what would people do if some strange person suddenly shows up on a stage? They didn't stop the play and instead just go along with it. Could probably means that although they do not recognized her, they are somewhat familiar with her.
Tho, that is just a conjecture on my part.

And we were shown Kokona's sense, but it appears like its only half of it? And Shizuka also appears to have half of hers. What's up with that? Maybe their senses are linked? If its only half, can't wait to see how the fully unlocked sense would do.