Hi @john john ,
1, You can organize the metadata in a way that makes sense in your business and use the metadata to make it easier to find what you want.
For more details, please refer to: https://learn.microsoft.com/en-us/sharepoint/managed-metadata
2&3, They should be determined according to your actual situation. But for SharePoint itself to limit the number of libraries:
Lists and libraries
2,000 lists and libraries combined per site collection (including main site and any subsites).
For more details, please refer to:https://learn.microsoft.com/en-us/office365/servicedescriptions/sharepoint-online-service-description/sharepoint-online-limits
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