I'm not sure there would be any difference between the two from a performance standpoint. I have not dealt with associations, but they seem like they are convenience objects for commonly used joins to other classes.
The way to determine for sure is to see what SQL is generated for a class join versus the equivalent association (e.g., create 2 reports, turn on DB Query events, and trace both). If the SQL is the same, then there is no performance difference. If the SQL is different, you can get an explain plan for each query to find out which is more efficient.
So I don't believe there is any performance difference between a class join and an association. The association rule is simply a convenience feature for defining a commonly used class join that is inherited by the descendants of the applies to class.