Automatically choose SSL Certificate based on accessed hostname in the same vhost

Use two server blocks, but move the common directives into a separate file. Pull the new file into each server block using an include directive. See this document for more.

For example:

server {
    listen 443 ssl;
    server_name nextclowd.raspi.local;

    # My self-signed SSL certificate
    ssl_certificate /etc/nginx/ssl/server.crt; 
    ssl_certificate_key /etc/nginx/ssl/server.key;

    include /path/to/common/config;
}

server {
    listen 443 ssl;
    server_name mydomain.ddns.net;

    # My Let's Encrypt SSL certificate
    ssl_certificate /etc/letsencrypt/live/mydomain.ddns.net/fullchain.pem;
    ssl_certificate_key /etc/letsencrypt/live/mydomain.ddns.net/privkey.pem;

    include /path/to/common/config;
}

Do not put the common file into a directory already used by nginx for wild-card inclusion, such as conf.d, sites-enabled and sites-available.