If a CA, who is otherwise acting good and participating in the Certificate Transparency system, were to issue a certificate without reporting it to any log, would this be noticed somehow?
I'm thinking the answer to this is no, but I'm not certain.
The only way I see that it could work is if the issued certificates themselves somehow are linked via hashes or something, but as far as I can tell that's not case.
(The log entries are linked via the Merkel hash tree, but that just stops the Logs from being manipulated)