Hi @sns,
Each web application corresponds to a content database. So, firstly check again and don't overview any web application in your SharePoint farm.
And except content databases, SharePoint creates other databases like configuration database(SharePoint_Config), CA content database(SharePoint_AdminContent_<GUID>) , web application databases. Be careful with them and don't delete them by mistake.
If you are sure that a content database which belongs to a deprecated/deleted web application, you can delete it then. No harm to your environment as per my knowledge.
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