Joanna eats 'the leavngs' in the kitchen, after everyone else has had their meal, along with Huck in his capacity as servant. There seems to be rather a disturbing significance to this. As her nickname 'Hare-lip' reveals, Joanna has a slight facial deformity, a cleft palate. The implication is that the family are ashamed of this, and so she isn't allowed to eat at the main supper table but has to eat afterwards, and apart, with the servants. This situation reveals the theme of discrimination, which is important to the novel as a whole. Joanna is treated differently on account of her looks, just as black people are treated differently because of their colour - although, of course, the prejudice in Joanna's case is much less marked. Just the same, it is there.
It is true that we are not explicitly told why Joanna is left to eat in the kitchen after the rest of the family, but there seems to be no other particular reason. It might be something to do with her age, that she is the youngest of the family, but her sister Susan is only a year older and doesn't have to eat in the same way. In any case, her nickname of 'hare-lip' does show a lack of feeling on the part of others.
Joanna, then, seems to be the victim of discrimination on account of her appearance, but it is not an issue that Twain explores. Her scene alone with Huck is played strictly for laughs, as she asks him all sorts of awkward questions about life in England, which he knows nothing about, although he is pretending to be an English servant.