We feed the Office 365 audit log into IBM QRadar for additional analysis, together with logs from firewalls, domain controllers etc.
If EOP puts an email into user quarantine or removes a email due to malware, does this event get written into the Office 365 audit log?
No. The audit log includes data from the Exchange admin audit log and mailbox level auditing, none of these include EOP events or mail flow in general. It's documented here: https://docs.microsoft.com/en-us/office365/securitycompliance/search-the-audit-log-in-security-and-c...
If you want to include such events, look into the mail flow data you can obtain via Get-Message trace or the good old reporting web service.