I don't know that any of that is evidence towards Neo's talents as JAPH, but here are my thoughts:
--It's obvious to all that he's some sort of hacker. I don't know exactly what he sold to that one guy, but he doesn't look like the stock-investment type. I would imagine that he sold him credit card numbers of some sort. That would lend me to believe that he's hacking into a lot of unix based systems. And what's the most rampant language on the average unix based system? Perl. I would imagine he'd want (or need) to know a bit of perl to do that.
--While the above evidence suggests that he might be a Perl hacker, it seems to me that he doesn't do that type of work for his company. The way he dresses for work, the way his cube-farm is laid out and the fact that his cube is so sterile lends me to believe that he works in a company that specializes in commercial software applications. I imagine there ain't much Perl happening in that company.
--He doesn't get out much...he didn't exactly look like he fit in that club. That alone says he's some sort of geek. And if he's a geek, he's gotta know perl. They're hand-in-hand, are they not?
All in all, does it matter? He isn't going to be doing too much perl now. After all, why program if you can simply CHANGE the matrix to do what you want.