"Listen in" is like "take", while "eavesdrop" is like "steal". For example:
She took a pencil from her coworker's desk
Without context it's impossible to say whether she is taking the pencil illicitly, or taking it because it's convenient. But if you say:
She stole a pencil from her coworker's desk
she clearly knows she's doing something wrong.
In the same way, if you "listen in" on a conversation, you're not necessarily doing anything wrong. It mostly depends on whether the speakers know they are being overheard, or if they expect privacy. For example:
Sitting alone in the cafe, she listened in on the conversations around her. Particularly interesting was a young couple quietly fighting over a pile of unwashed dishes, which apparently one of them had promised to do some days ago.
In this context, "listen in" is slightly naughty, but since it's a public cafe there's not really any expectation that conversations will be private. However, if instead you wrote:
Sitting alone in the cafe, she eavesdropped on the conversations around her.
This is definitely naughty, as she knows the conversations are not meant for her ears, but she's listening anyway. Same context, different nuance.