What they did was illegal. Unless the warrant specifically stated it was for the search of pirated software, they had no right to confiscate 'em or try to press charges on you. The cops are simply looking for a 'fall guy'. They can't find the real one, they're being pressured by many sources to find the guy, and at that point, bringing ANYONE in that could be vaguely accepted as the thief is OK in their eyes.
Get a good lawyer (do NOT skimp on the cash here.... drop out and get a job or two, if neccessary), and do not accept any deal they make with you. If you didn't do it, and you're not just trying to get out of a crime you commited, you'll win, providing you got enough cash and a lawyer that actually has balls.
Note on my advice: You may be wondering why I told him to drop out if he has to. Yes, education is worth alot, but you can barely get a job at McDonalds with a criminal record that has a theft charge on it (especially one that's larger than $500). So he could take two routes: cave in, get charged, serve time, persue his education, and eventually have a Bachelors in Electronic Engineering (for example), but be unable to get a job, or he could fight it, possibly have to drop out, get out of the bogus charges, go back to school, and get on with his life, so that EE degree can actually get him a job and, therefore, advance into life as any adult knows it.
Yes, legally, once he turns 18, the record is wiped clean. However, the charges can still be pulled up if an employer/cop really wants to, it just costs a little bit of cash (I know that for a hard-lined fact).