Does MVC architecture design pattern effect MySQL database performance?
We use cake for some internal applications.  And yes it does at times, pardon my french, suck.  This isn't anything to do with mysql per se.  Once you start defining more than basic models and go down the "has many"/"has many belongs to many" relationships, the underlying queries it generates can be less than sub par.  

Do you have table with multi column primary keys? Forget about it.

Frankly there are just times you need to break the molding your framework is supposed to shield you from and write your sql more directly :-\

That being said, as with anything else interacting with your DB you'll want to ensure you have proper indexes and appropriate buffer pool/key buffer.