The CRM integration does not clean up any duplicates that originate either in Salesforce or Acoustic Campaign.
If you have a duplicate mess in your CRM, expect it to be recreated in your marketing database when synchronized. The integration is only a bridge. If you have a lot of dupes in SFDC, then the integration will recreate them in Acoustic Campaign. If SFDC is loaded with duplicates, it might be a good time to clean them up before you synchronize to syncing with Acoustic Campaign. Once the integration is live, it is recommended to implement duplicate prevention techniques in both the applications to keep duplicates to a minimum. When duplicates occur, merge inside SFDC. The integration will handle the merging of the corresponding Acoustic Campaign records.