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.