Beyond the already known SMTP problem (I have a PMR open on that) I found more problems:
After creating a new SHA-256 certificate for a Domino 9.0.1 FP2 IF2 server with 4096 (!) bits key length I found that both DIIOP and LDAP were no longer accessible via their SSL/TLS ports but HTTPS, IMAPS and SMTPS/STARTTLS were working. I could connect and retrieve the certificate successfully using a command line openssl client from these three ports but not from LDAPS and DIIOPS. Also, DIIOP gives an error message about not being able to load a certificate from a temporary file while starting. The file with the reported name briefly exists in the temp directory but is very quickly deleted again.
After creating yet another new SHA-256 based keyring with a 2048 bits key, LDAPS and DIIOPS were also accessible via openssl check again. However, I can still not really interact with, for example, the command line ldapsearch tool from my Notes client with the LDAPS service. I have no quick check tool available for DIIOPS ... also, DIIOP still gives the error message at startup about not beeing able to load from that temporary file.
It could well be that at least LDAPS has a similar SSL/TLS negotiation problem like SMTPS/STARTTLS.