The Padres have declined their $4 million option on Josh Johnson, but he's not a good bet to become a Pirate anytime soon.
First, and most importantly, it appears fairly likely that Johnson will re-sign with San Diego for a lesser amount -- he feels he has "unfinished business" with the Padres after having Tommy John surgery early last season. In the past, he's also preferred to pitch on the West Coast, turning down more money elsewhere last year to sign with San Diego.
Second, as someone (it might have been Vlad) pointed out in the comments last year, there's a difference between the sorts of buy-low pitchers the Pirates usually like (mostly hard throwers with out-of-sync peripherals and the ability to get ground balls) and Johnson, who's just hurt all the time. The Pirates pursued him last year, but I'm not sure I expect that to happen again this offseason. At some point, the injuries are just too much. Johnson is great when he's healthy, but he's thrown more than 82 innings in a season only once since 2010. He's seemingly had trouble with every part of his arm, with shoulder, triceps, forearm and elbow injuries in his past. Maybe Johnson will return next year and be great, but the Padres declining a modestly-priced option suggests that he won't. My guess is that he'll wind up in San Diego again.