Happy is like Natsu's son, so of course it's not going to be easy for Lucy to replace him. But Lucy doesn't have to replace Happy, because the three of them are a family. Lucy may not have been there to comfort Natsu when Igneel died, but she knows how much Igneel meant to Natsu. It lead to a pretty sweet moment where she was watching him sleep. When Igneel appeared, Lucy showed her concern at Natsu before he ran off. Also keep in mind that Lucy had also lost Aquarius during Tartarus, and usually it's Natsu that comforts her.
I mean, if you hold this against NaLu, you gotta use the same standard for other pairings. How much does Lucy know about Silver? During Tartarus, Lucy never found out about Silver being Gray's father. I'm not sure if Lucy even knows Silver's name to this day. This is ignoring the fact that Silver downright handed Gray off to Juvia.