Currently the performance nag is shown to the user whenever the plugin detects that the site has been viewed over 400 times within the last hour or so. This is a good indicator that a site has some traffic but it doesn't cover uses cases like small sites accumulating a lot of views over time.
It might be a good idea to also run a query like the one below to check whether the summary table has reached a number of rows (eg. 1 million) so we can alert users about it:
SELECT
TABLE_ROWS AS 'rows'
FROM
information_schema.TABLES
WHERE
TABLE_NAME = 'wp_popularpostssummary'
AND
TABLE_SCHEMA = 'database_name_here';