Thanks Aleks,
I followed @jibecfed suggestions at Onion et yunohost - Some questions in order to avoid leaking some data on the certificate. So I created subdomain.domain.tld, convert the subdomain into the main one, uninstalled the app and install it again.
So now I guess I should not import /etc/ssl/certs/ca-yunohost_crt.pem into the client, but a new certifcate that I guess it has been created because of the new main domain.
Am I right?
If so, where is the new certificate I have to import?