Doesn’t matter what method you use (manual, webroot, standalone…), your server is not answering requests to your IPv6 address and as @bytecamp said, Let’s Encrypt will try to validate your domain using IPv6 address if it is present.
Trying to connect to your mail server using IPv4 -> OK
$ telnet -4 mail.ex-nihilo-paris.com 25
Connected to mail.ex-nihilo-paris.com.
Escape character is '^]'.
220 mail.ex-nihilo-paris.com ESMTP Postfix
221 2.0.0 Bye
Connection closed by foreign host.
Trying to connect to your mail server using IPv6 -> TIMEOUT
$ telnet -6 mail.ex-nihilo-paris.com 25
telnet: Unable to connect to remote host: Connection timed out
Trying to connect to your nginx server using IPv4 -> OK
$ curl -4IkL https://mail.ex-nihilo-paris.com
HTTP/1.1 200 OK
Date: Wed, 27 Dec 2017 15:12:29 GMT
Cache-Control: no-store, no-cache, must-revalidate, max-age=0
Trying to connect to your nginx server using IPv6 -> TIMEOUT
$ curl -6IkLv https://mail.ex-nihilo-paris.com
* Rebuilt URL to: https://mail.ex-nihilo-paris.com/
* Trying 2001:41d0:203:1d8::...
* TCP_NODELAY set
* connect to 2001:41d0:203:1d8:: port 443 failed: Connection timed out
* Failed to connect to mail.ex-nihilo-paris.com port 443: Connection timed out
* Closing connection 0
curl: (7) Failed to connect to mail.ex-nihilo-paris.com port 443: Connection timed out
Are you sure your IPv6 address is correctly configured? Because for me,
2001:41d0:203:1d8:: looks like an anycast address.
Or you remove the AAAA record for domain
mail.ex-nihilo-paris.com or configure your server and/or AAAA record correctly so your server can be reached using IPv6.