The mod detection I've heard of is similar to what M$ is doing on the Xbox. XBLive uses a BIOS checksum to see if a "Hacked" bios is being used. If the checksum is valid, you're alowed on (orig BIOS). If it's invalid, you get banned (Hacked BIOS).
Now, because Sony does not controll the online aspect of the PS2, it's up to the developers to implement this type of detection. If I remember correctly, SoCom has mod detect (probably in the way of BIOS checksum or something similar), and if it detects a mod, you are not allowed to join the online portion of the game. But, you are not banned. If you remember PS1, there were similar problems. When FF7 was released it had mod detection built into it. But, because the detection remained on the disk, it was easily crackable (Stealth Mods). Sony's (or the developers) method of detection is going to be much easier to crack. You will eventually see "Stealth Online Mods" or patches that remove this part of the game.
Xbox Live is going to be much harder to crack. XBLive mod detection, once cracked, can be changed to look for something else. They could do this, and still have it affect already published games. Once Sony published a game, and it's cracked, they can't go back and change it. They must republish the game.
Now, don't quote me on the SoCom thing becuase I haven't played and PS2 games online at all. And, they could just be testing this in certain areas (Japan most likely) before doing a full rollout of this. Yes indeed, most games do work, if not all. But don't expect things to stay the same.