There is no official ini file specification, therefor control codes are neither supported not unsupported in the file format itself. The ini file format is a very old configuration storage method that was surpased a long time ago, though never fully abandoned (obviously).
While it may not (im not certain) be natively supported by many API's or by microsofts API's, it is certainly not something that can not be done or that is a limitation of the format. Rather, it is a limitation of the API (or custom routine) used by the application/programming language.
There is an unofficial specification here: http://www.cloanto.com/specs/ini.html
So basically this is a limitation (or intentional behavior?) of mIRCs routines and not of the file format itself.
There are definately other programs that utilize an ini file storage method and handle control codes just fine. (a common example of this is flashfxp)