StackOverflow is not SaaS!
Well, I guess that could be argued, given that the SaaS moniker has been abused so much that nobody really knows what it is any more, but without going into a pages-long theoretical debate about the definition of SaaS, suffice to say "SO is just a website, no fancy-pants acronyms here thank you very much (IMHO)"
This is tangential to the question anyway. I too would be curious to find out answers to things like 'how much can you impede the customer', whether you call it SaaS or not. I don't know anything about the market, but I have some suspicions as to what the answers will be:
How has the growth of SO impacted traffic to JoS/BoS/DoS?
I'd be surprised if it had impacted at all
How has the inclusion of advertising on SO affected revenues?
Without advertising, SO would have no revenue, so the effect is that revenues have increased by infinity percent
How has the inclusion of in-line advertising on SO impacted traffic (or maybe reduced the growth curve) if at all?
I don't know if this is something you can measure at all until you get to the scale of google
What is the proper balance of "impeding the customer" and advertising to maximize both profits and traffic?
"It depends on who your customer is" - if you have a large base of uneducated idiots, their tolerance for advertising will likely be quite high, and vice versa of course
Are you better off maximizing profits by charging for answers like some of the subscription Q&A sites, even though it reduces traffic and search engine exposure?
Only if you place no value on goodwill or the longterm health of your site