Will there be a performance impact if there are 100 million Linked Content Entity?

The module does not provide a pager or mechanism to effectively fetch 1000 or more rows. It only provides some Twig functions and tokens that can be used. In this case, you would have to implement a function yourself that fetches this amount of rows. In the admin overview, the default pager of the "List builder" is used.

Is there a specific use case where you load 1000 or more rows?

I found that it stored in a configuration file, so it should not be able to create too many tokens, such as 1 million, as having all of them in one configuration file would make the file very large. Of course, I'm not sure if it's suitable for storage in the configuration.

I mainly use it to establish indexes with entity articles, such as specifying an alias to bind an article, and using this alias to find the ID of the article. This is very useful in some places where the node ID cannot be obtained from the current page, such as when loading Ajax, the current page token cannot be used, only the global token can be used.

Establishing an index in this way will create too many rows of data, It needs to be stored in a table, not a configuration file.