My view as a heavy ebook reader: ePubs should be inert data. No javascript, no interactivity, no network resources. Just a fancy text file with some appearance settings all of which the reader can override.
Don't confuse what's necessary for standard fiction books with what the format should support.
JS and interactivity are fine, in technical books, reports, or niche fiction.
What I absolutely agree on is that epubs don't need is networking. Resources on the internet get stale after years or decades anyway, so inclusion of any network assets into an epub guarantees that the work will degrade over the years. References can be web links, but nothing from the internet should be embedded.
a) What epub editor software allow direct editing of MathML, and is it a good idea to depend on such software being available in order to edit the book without tinkering directly with the MathML by hand?
b) Does MathML support everything mathjax does?