CodeIgniter switching driver from mysql --> mysqli

Question

I was reading this question: The mysql extension is deprecated and will be removed in the future: use mysqli or PDO instead

And it got me thinking that I should make

Answer 1

Are there certain queries that are treated differently?

No.

The MySQL and MySQLi extension are “drivers” that take care of the communication between PHP and the MySQL database server;

they do not change the range of SQL commands that the MySQL server understands.

So as long as the DB abstraction layer takes care of what PHP functions are to use for what purpose for you (and a framework like CI should most certainly do that), there is nothing to worry about in regard to the actual queries.