I think it's possible she didn't know but I would imagine that either Trask or Wayne Irig mentioned the color of the rock to her.

Quote
Might be the reason why some goons tried the red variety on Superman. Had they known that kryptonite is supposed to be green, they might have ignored the red rocks altogether.
The red kryptonite showed up for the first time in Individual Responsibility and Billy Church did mention that it was supposed to be green but Gene Newtrich explained that its chemical properties revealed that it was, in fact, kryptonite. They weren't sure what it would do so they tested it on Supes.

Fanfic | MVs

Clark: "Lois? She's bossy. She's stuck up, she's rude... I can't stand her."
Lana: "The best ones always start that way."

"And you already know. Yeah, you already know how this will end." - DeVotchKa