using drush php-eval db_query() are there differences with db_query() from code?
I don't know this for definite but conceptually speaking, if Drush didn't use a standard Drupal bootstrap to perform these tasks it would have to re-implement all of that functionality itself.

Drush uses your site's settings.php file for the database connection, which leads me to believe it will also have access to things like $db_prefix.

I think it's safe to say exactly the same thing is happening when you run db_query() from Drush as if you run it from any other bootstrapped instance of Drupal.