What is the SEO effect of hosting a .NET site as examplesite.com on Amazon AWS EC2/RDS, and Wordpress site as a subfolder: examplesite.com/subfolder with a different hosting provider?
In general no effect... and...
Be aware all content in subfolders + subhosts is now considered part of domain, so make sure you stick with some sort of common theme across all your content... to maximize your SEO.
Also, there's no real way to do what you describe... short of using sshfs or something similar to mount your WordPress site into your EC2 instance, so technically you'll have challenges.
Likely best you talk with a Server Savant about what you're targeting to accomplish, before you get to far down your implementation track.
Also, you'll have far more flexibility if you dump your .net tech + go with strait up LAMP...
Linux + Apache + MariaDB + PHP + WordPress.
With .net you'll end up spending considerable time trying to fix technical issues that are unfixable or take many times the hours + dollars required to fix with a Lamp Stack.
Generally speaking it has no effect. My name is Humberto Valle, I'm an MBA and marketing strategist for http://Unthink.me for almost 10 years. I deal with SEO often. The thing you have to consider with SEO is that for development you simply need to make sure that your page structure is well thought out and easy to follow, XML sitemaps are key for good SEO and having easy flows and hierarchies allows for search engines like Google to index you a lot easier and faster which yields higher exposure. Best of luck, if you are looking for more SEO advice or help check out our blog, we have some handy posts there.This one for example is for SEO Newbies, if that's your case. http://blog.unthink.me/how-long-does-seo-take