I have to agree.Yeah. I saw that not as "she literally could not see them". I think if they had wanted us to get that idea, they'd have shown it explicitly.
Wanda knows little or nothing about magic. She thinks she has superpowers. He is just boggled and scared by the whole situation.
We as the audience cannot see the runes/spells until Agatha reveals them in that scene either. If they were meant to be visible, and therefore something Wanda should have noticed, then we, the audience, should have been able to see them in advance. This would then contrast our knowledge with what Wanda demonstrates on screen.
The fact that we cannot see the spells until they are revealed to Wanda means they are warded/invisible to the naked eye.
I think Agatha's comment is more supposed to be in the line of "if you were a true witch you would have had your true-seeing spell up at all times to identify spells" or perhaps "if you were a true witch you would have known to expect magical wards around a sanctum such as this amd would have been looking for them."