The PS2 is a relatively unhacked fairly modern/powerful console without much in the way of great hardware specs, debugging emulators or work done on the files and formats involved.
Still the isos themselves are twofold.
1) The plain iso as can be modified/extracted via poweriso, ultraiso. 7zip and whatever else.
2) The raw LBA (if you read some of my older posts I said DMA a lot, technically not inaccurate but use LBA in future discussions). These are files written outside what the plain iso stuff can see. Why this was done we can have a nice little debate over but the fact remains it was frequently done (not always but often enough that I mention it), Square (Enix) were quite noted for it.
Once you have that sorted it is the same as every other console ( http://www.romhacking.net/start/
) albeit without the benefits of a debugging emulator, well developed tools and for a system that can quite easily handle high level scripting.