The popular "Bonnie Prince Charlie" in this spelling may be the source of two possible exceptions

More likely the result of it. He wasn't often referred to that way in his lifetime - it's a 19th century label.

I think Burns may have preferred "bonnie" and he would have been influential. Scott seems to have spelt "Bonn[y|ie] Dundee" both ways before settling on "-ie".

In manuscripts from before 1700 I've sometimes seen "boñy", which is a hangover from mediaeval orthography.