I don’t think Haibara is happy that Kudo didn’t confess because she likes him, I think she is just happy that he still has to stay as a kid. She said in chapter 189 that the only reason she is able to stay calm and live her life hiding as a kid is because Kudo is right next to her in the same position. She just doesn’t want to be alone. Plus she already told Ayumi that she doesn’t see Kudo romantically in chapter 201
By the way it totally didn’t take me like 40 minutes to find those chapters as proof, I totally didn’t do that...