In fact, pandoc now does have an ipynb reader and writer. You can convert between ipynb and any of the formats pandoc supports, and you can manipulate the AST using filters.
My main concern with jupyter is that I prefer orgmode (and by a lot), but I know that it's niche and most people don't even heard about it ipnbs are preferred form of notebook exchange.
I will check how good translation to/from orgmode is then.
