Hello Mark. I'm Joelma from Brazil. So these three words are very similar and are synonyms. You are right about the meanings (assunto - subject, tópico - topic, tema - theme). So, in general, these words indicate what is being talked about. E.g.
Qual o assunto do seu livro?
Quais tópicos seu livro aborda?
Qual é o tema do livro?
I hope that was useful. :)