Hey @LLampe, check out this Knowledge Base article from HubSpot, notably:
You will not have the option to merge company records if your account is integrated with Salesforce. To clean up duplicate records in HubSpot while the integration is installed, you can delete the extra duplicate companies in HubSpot using the duplicates management tool. Ensure that you keep the company in HubSpot that syncs to the primary account in Salesforce. If you have duplicate companies syncing from Salesforce, you can either merge the accounts or delete the extra duplicate accounts in Salesforce.
The Deal merges and following sections should also help you out with merging your deals.
Hope this helps!