No, sys.id is not unique per se. A globally unique identifier of a record is defined by 4 parts: (1) space ID, (2) environment ID, (3) entity type (entry or asset), (4) ID (sys.id)
It could be due to that the API token you use doesn't have access to the environment, you could go to 'Settings' -> 'API Keys' -> 'Environments' to check and configure it.
You could use the Content Delivery API:
Retrieve all the entries/assets
Perform an iterative process through all the entries/assets utilizing links_to_entry & links_to_assets query parameters
The entries/assets that aren't linked to any entry return "total": 0 in the API response
The process might be costly, but it should be feasible if it is for housekeeping purposes.
It is not directly possible via REST API, you will need to perform two requests to achieve so. Alternatively, it is possible to use GraphQL for OR operation, please find the documentation here.
You could use the inclusion operator, for example:
?sys.contentType.sys.id[in]=content_type1,content_type2,...
You can query an entry and its related data in a single request with include parameter, since the parameter is only available for the entry collection endpoint, you could use a query like: entries?sys.id={entry_id}&include=5
You can query an entry and its related data in a single request, however, if the linked items are unpublished or deleted, they will not be retrievable through the Delivery API and, as a consequence, a notResolvable error is returned in the API response.
You could use sys.publishedVersion[exists]=false in Content Management API to filter these entries. Entries that are never published don't have sys.publishedVersion attribute.