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

No Effect for Separate Site in subfolder on a different server

If the WordPress site or blog is in a folder of the main domain, you'll reap SEO benefit.

It's when you place the WordPress site in a subdomain then you start to lose SEO value, reporting options, and a cohesive experience for your visitors.

I encourage my SEO clients to use folders and I do what I can to avoid subdomains.

There is no benefit to hosting the main site on one hosting configuration, and the separate subfolder site on another hosting configuration. I think I know why you are asking this (related to C-blocks), but I would advise hosting both the main site and subfolder site on the same hosting, as Google will look at it as part of the same site anyway. Kudos for going for the subfolder route - you lose some SEO benefit when you go the subdomain route.

Search engine optimization (SEO) is a catch-all term for the steps you can take to improve your website’s rankings on search engines. Most of your Internet traffic will come from searches performed on search engines like Google. When your website appears above your competitors on search engines for the products and services you supply, you can dominate the market. Website owners, therefore, spend enormous amounts of time and money performing SEO on their websites. This can include creating relevant content, optimizing pages so they are easy for search engines to read, and building up the number of inbound links from authoritative websites.
SEO effect of hosting .NET site on Amazon AWS EC2/RDS, and WordPress site as a subfolder can be as follows:
1. Slow website speed: If you choose a cheap website hosting company, then your website may load slowly for visitors. Apart from making for poor customer experiences, a slow website will be penalized by search engines, making your rankings in results drop. Google has specified that the time a website takes to load is an important factor it considers when deciding the order, it lists sites on search engine results. A good website host will have excellent networking infrastructure and will not host too many websites on the same servers, helping to keep your website running fast. You also need to consider ways you can optimize your pages, so they load as quickly as possible. This includes removing redundant scripts, compressing images, and stripping out third-party widgets you do not use. Google Webmaster Tools can be used to diagnose and address the cause of website speed issues.
2. Website downtimes: Worse than a site that loads slowly is a site that doesn’t load at all. When your site is unavailable, it makes for a terrible customer experience and your potential buyers will simply go to your competitors. If your website goes offline because of issues caused by the web host, you can be sure that search engines will take note. If your site is frequently unavailable, Google will flag it as unreliable and therefore unlikely to offer the excellent customer experience they try to promote. Your site will drop down the search engine rankings. If your website goes offline for an extended period, it will be dropped from search engine results completely. When shopping around for a website hosting provider, note companies that guarantee a certain uptime percentage. The best website hosts will guarantee your website will be up 99.99% or even 100% of the time.
3. Database connection failures: If you’ve ever seen an Internal Server Error or Database Connection Failed message when you have tried to visit a website, this means the website is having problems accessing the files needed to display content to you. It could be a configuration error, but often it is caused by a database being concurrently accessed by too many people. This can happen when an article or video has gone viral on social media and thousands of people are trying to view it at the same time. Good hosting has safeguards to make sure servers do not get overloaded. Files are cached on alternative servers and popular pages can be offloaded so that the number of connections to the database is reduced. Upgrading to a virtual private server (VPS) or dedicated server is another way to increase reliability and durability. With a VPS, your website is allocated a set share of the web server’s resources, so if another website on the server experiences a rapid boost in traffic you will not be affected. If you use a dedicated server, you will have the entire server to yourself.
4. Using shared hosting services with spammers: If you use shared hosting, it means your website will be on the same server as hundreds or thousands of other websites. If any of these other websites are run by spammers, scammers, or other nefarious types, the IP address may be flagged as malicious. Your website’s search engine rankings could drop like a rock if it’s considered to be in a bad neighbourhood.

A good website hosting company will immediately kick spammers from their servers, minimizing the chance of this happening. If you would like to check which websites, you’re sharing an IP address with, you can use a reverse IP lookup service.
5. Incorrect TLD: Top-level domains (TLDs) are the parts of the domain that come after the dot (e.g. .com, .net, .org.) Though there have been attempts to popularize other TLDs like .co, most people still expect your website to have a .com TLD. Using other TLDs makes your website harder to remember and can cause a loss of traffic. TLDs do affect Google search engine rankings, but not by too much. The TLD of a website is just one of the hundreds of ranking factors Google uses to rank websites, but using a .com TLD will help your SEO efforts because your website’s name is more memorable, making it easier for people to share with others. If you are targeting a specific country, using a geographic suffix such as co.uk is a reasonable alternative to .com, as Google will boost your website in local results.
Besides if you do have any questions give me a call: https://clarity.fm/joy-brotonath