The latter. Creating millions of dynamic tables for this use case is not what SQL databases are designed for.
If you create a foreign key relationship from the clues table (column questionID) to the question table (column ID), the database will even guard for you that each clue actually has a valid question associated with it. What's more, if you setup cascading deletes 9n that foreign key relationship, you only need to delete a question row and the clues will automatically be deleted for you. As you can see, this type of relationship is best modeled this way. There are many more reasons why you should do this, but I'm hoping this gives a beginners overview.