1) why would so many companies like Hubspot, others require email for content exchange if putting on site would do as well?
Here are two answers:
A) they want to spam you with email and sell your email to everyone on the planet;
B) the value of a sale is enormous, so they would rather have a sale than the ad clicks
Does the type of industry: B-B, vs B-C make a difference in how you would approach or is your answer blanket for all types B-B,B-C?
Publishing for everyone makes more sense for the B-C business because the number of potential visitors is enormous compared to the B-B.
If we go the route of publishing to site (not pdf) does it make a difference whether a 12 page ebook is one long scrolling page or should the content be 'click to read more' which advances to another possibly optimized page? If multiple pages then each page would likely be optimizing for pretty much the same content?
I put a few thousand words on a page but if you have more then I would break it into separate pages. I would break the ebook into chapters or lessons each targeting a different keyword.
Has there been any correlation between top step (main menu) and 2, 3, 4 steps below the main navigation on relevance (with same content) in rankings?
Yes. The deeper you bury the content in your navigation the deeper it will rank in the SERPs. If you want to promote this for traffic, income, links, tweets, signups, I would think that you would be showing it to every person who visits your website. That's what I do when I have something hot, valuable and important. If you fail to do that you lose the opportunity.