AWS S3 VPC endpoint docs example
Based on the "Example: An Endpoint Route in a Route Table" in
http://docs.aws.amazon.com/AmazonVPC/latest/UserGuide/vpc-endpoints.html
Once the S3 VPC endpoint is applied, all traffic destined for S3 in that same region goes through the endpoint while all other traffic goes through the IGW.
Assuming that I have the same setup but in a private subnet and for all other traffic I am using a NAT(in a public subnet with IGW) and not IGW, would the traffic destined for S3 still go through the S3 VPC endpoint or would it be going through the NAT?
It will go through the endpoint not through NAT. The VPC endpoint is for all subnets in the VPC - whether it is private or public doesn't matter. private connection between your VPC and another AWS service without requiring access over the Internet, through a NAT device.
How did you miss the diagram in the same page you mentioned? It shows clearly the traffic from both types of subnets go to the S3 endpoint without NAT or IGW.
