Prince John had severe epilepsy and was probably on the autism spectrum, but wasn't badly treated, Jalima. In fact it seems that he got more affection from his parents than his siblings did. He was well cared for on the Sandringham Estate and actually not really hidden away - he appeared in official family photos and there are stories of the rather embarrassing things he said to visiting dignatories. It would be a nice tribute to him if the name could be revived.
The Princes in the Tower were Edward Vth and his younger brother Richard of Shrewsbury. They were of course declared illegitimate by their paternal uncle, who might really have believed this bearing in mind Edward 1Vth's previous betrothal before his marriage to Elizabeth Woodville. Henry V11th re-ligitimised these children by rather devious means in order to marry their sister. No wonder he got so worried about Perkins Warbeck!!