In general, the rule that you mentioned is correct. In this case, however, the meaning of your first sentence is pretty clear. "My parents have two glasses of milk every morning" is not very clear. It makes me think that your parents each drink two glasses of milk. In my opinion, these are the best options: "My parents each have a glass of milk every morning" or "My parents both have a glass of milk every morning".

It's ok. If the writer wants to be really clear, then it should be "My parents each have ...". On its own, although the original sentence is a bit vague, the implicit meaning is each parents have one glass of milk. If this was a formal piece of writing, for example a written experiment or a statement to a lawyer, then you must write 'each parent'

Colloquially, I think it's fine and it would be understood what you mean, since it is unlikely that your parents would share a single glass of milk (however that too could be possible), but if you want to be more clear, you could add the word "each" to be more precise. If you were to say "My parents have two glasses of milk every morning," then I would end up assuming that they have two glasses each. Also, whether both the subject and the object will be plural depends on the context. It will not always be so.