The jdk.tls.disabledAlgorithms property also applies to certificates, as the definition states in the java.security file:
# For PKI-based peer authentication and key exchange mechanisms, this list
# of disabled algorithms will also be checked during certification path
# building and validation, including algorithms used in certificates, as
# well as revocation information such as CRLs and signed OCSP Responses.
# This is in addition to the jdk.certpath.disabledAlgorithms property above.
This functionality is not currently working properly.