The way I see it, she doesn't care much about that room and his discovering it, what is important is that they share this secret. At one point she might dislike that fact that he saw it, but on the other, she's a Yandere, she loves him even more now that he knows one of her secrets.
Eh those Yandere's ...
Can't live with them, can't without them.
Also, Yuno works hard to do what she promised to do, to the point of overexerting herself.