So was this the case, i.e. all bugs against LibreOffice Online shall be filed on GitHub from now on?
Yes pls do. Sorry for the confusing situation 
Would it make sense in this case to remove the “LibreOffice Online” product from the Documentfoundation Bugzilla?
That is something for TDF and people managing BugZilla there. Unless you are involved there, I would just leave and see what comes up.
Shall I re-report recent bugs currently filed in Bugzilla but relevant for CODE 6.4 on GitHub (and somehow link the issues)?
To be honest, I do not know if there is a general policy here. prolly @kara… does know?