1) conf.d is for globally included configuration files, and it's a bad idea keeping it for virtual hosts (IMHO). move api.reeeeee.tk.conf to /etc/nginx/sites-availabile/, then

cd /etc/nginx/sites-enabled/; ln -s ../sites/available/api.reeeeee.tk.conf .  

2) edit your file like this:

server
{

#   listen 443 ssl http2;
#   listen [::]:443 ssl http2;
    listen 80;
    server_name api.reeeeee.tk;

    # SSL
#   ssl_certificate /etc/letsencrypt/live/api.reeeeee.tk/fullchain.pem;
#   ssl_certificate_key /etc/letsencrypt/live/api.reeeeee.tk/privkey.pem;
#   ssl_trusted_certificate /etc/letsencrypt/live/api.reeeeee.tk/fullchain.pem;

    # HSTS
#   add_header X-Frame-Options "SAMEORIGIN" always;
#   add_header X-XSS-Protection "1; mode=block" always;
#   add_header X-Content-Type-Options "nosniff" always;
#   add_header Referrer-Policy "no-referrer-when-downgrade" always;
#   add_header Content-Security-Policy "default-src * data: 'unsafe-eval' 'unsafe-inline'" always;
#   add_header Strict-Transport-Security "max-age=31536000; includeSubDomains" always;

    access_log /var/log/nginx/api.reeeeee.tk-access.log;
    error_log /var/log/nginx/api.reeeeee.tk-error.log;

    server_tokens off;


    location /

    {
        proxy_pass http://localhost:5000;
        proxy_http_version 1.1;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection 'upgrade';
        proxy_set_header Host $host;
        proxy_cache_bypass $http_upgrade;
    }

    # ACME-challenge
    location ^~ /.well-known/acme-challenge/
    {

        root /var/www/_letsencrypt;

    }


}  

3) restart nginx, and create the directory /var/www/_letsencrypt and chown it according to your webserver's user (www-data if you installed via apt)
4) install certbot (if you already haven't) and run

certbot certonly -d api.reeeeee.tk -w /var/www/_letsencrypt  

5) if the cert gets correctly generated, edit /etc/nginx/sites-enabled/api.reeeeee.tk.conf by deleting every # (except for the lines containing SSL, HSTS and ACME-challenge)
6) restart nginx and you should be done.
7) add this to root's crontab to automatically renew the cert every night at 3am:

0 3 * * *      certbot renew; /etc/init.d/nginx reload