I believe how it works is:
It throws up an anti-Piracy message.
Sends vastly more enemies your way- even enemies that normally don't appear in the area. For example, Spiteful Crows appearing in vast numbers in the Sphinx area near Scaraba.
Crashes the game during the Giygas battle, deletes all saved games.
I've played on a ROM before, and nothing happened on any count for me- I believe if the first 2 don't happen, you should be good.
Oosta!
Never underestimate the power of the nerd!