One possible reason could be that Snape has some hidden knowledge or magic that allows him to communicate in such a way. Maybe he's trying to protect Hermione secretly and this mind - talk is a discreet way to give her advice without others noticing.
It might be related to Hermione's own magical abilities. Perhaps she has an untapped potential that Snape is able to connect with on a mental level. He could be drawn to her intelligence and want to guide her in a more personal way. For example, he sees her as a key figure in the fight against the dark forces and this mind communication is a way to train her without drawing attention from the wrong people.
It could make her more confident. Knowing that Snape, a powerful and complex wizard, is communicating with her privately gives her a sense of importance. This might lead her to be more assertive in her actions and decisions.
One possible reason could be that Snape sees Hermione's value as a brilliant student. He might recognize her potential and not want it to be wasted just because of her dad's actions or situation. Maybe he has a sense of justice deep down, despite his often cold exterior.
Perhaps she's being bullied. In the wizarding world, there could be other students who pick on her because she's a 'Mudblood'. This could be really distressing for Hermione, and when Snape finds her crying, he might be conflicted between his general dislike for Gryffindors and his sense of justice.
One possible reason could be a misunderstanding. Maybe Hermione thought Snape was involved in some dark plot against her friends. In the wizarding world, there are often secrets and deceptions, and if she got some false information, it could lead her to take such drastic action.
Hermione could be hiding her pregnancy from Snape because she's not sure of his feelings towards her. There may be an ambiguous relationship between them. She might be in love with him, but not sure if he feels the same. And she doesn't want to burden him or make things awkward between them. Or perhaps she suspects that Snape might be involved in something dangerous, and she doesn't want her unborn child to be dragged into it.
Perhaps she was poisoned. There are many dark potions and substances in the wizarding world. It's possible she accidentally ingested something or was targeted by an enemy. Snape, being a master of potions, would be the most likely person to figure out the antidote and heal her.
It's unacceptable because it violates the power dynamic in the 'Harry Potter' world. Snape is a teacher and Hermione is a student. This kind of inappropriate interaction goes against the basic moral code of the series.
Maybe Snape made a snide comment about Hermione's intelligence or her Muggle - born status. Snape has a rather acerbic tongue, and if he said something derogatory about Hermione's abilities or her heritage, she would surely be furious. After all, Hermione works extremely hard to prove herself in the wizarding world and any attack on her intelligence or background would be a big blow.
One possible reason could be the stress from her studies. Hermione is always under a great deal of pressure to excel academically. Maybe she reached a breaking point due to the overwhelming workload. Another reason might be some kind of conflict with her friends. For example, if she had a big fight with Harry or Ron over something serious, it could leave her feeling broken.
One possible reason could be a powerful spell gone wrong. Maybe she was caught in the crossfire of a dark magic spell that Snape was either trying to counter or was involved in accidentally. Another reason might be extreme emotional shock. For instance, if she discovered some dark secret about Snape that was so overwhelming it sent her into a catatonic state.