Baseball players aren't arbitration eligible until they've completed three full big league seasons. They're indentured -- basically meaning the teams can pay them whatever they choose. Then (like in this case) teams generally sign players to a bigger deal to avoid going to arbitration in their 4th-6th years with the team.
He definitely deserves it. One of my favorite Horns on my favorite team. I'd be surprised if he's still with the A's beyond July 31, though.
He also rec'd a signing bonus of almost a million bucks three seasons ago, so it's not like he's been scraping by on just $350,000 per year.