Even the drug dealer is mostly not going to get rolled for in my games. If you have a rogue in the party, or anyone with an appropriate background, you'll find a guy. Those dudes are much like merchants in that they sort need to be available and findable to some degree. Now if you want to find an assassin, that might be trickier.
Another option for a completely urban campaign, is to change how those seemingly worthless skills work to reflect the setting. Survival in an urban setting tracks pretty flawlessly onto what might in another system be called Streetwise and Area Knowledge, for example. Nature is a little tougher, but I'm sure you can think of something in a pinch. I'd probably call it something to do with factions and politics and reading the political currents, maybe even knowing who's who. I know that doesn't sound much like 'Nature' but it is, given a level of abstraction, the Nature of a city, the beating heart that drives it's growth and decay. Anyway, the point is that there are lots of cool options.
Another option for a completely urban campaign, is to change how those seemingly worthless skills work to reflect the setting. Survival in an urban setting tracks pretty flawlessly onto what might in another system be called Streetwise and Area Knowledge, for example. Nature is a little tougher, but I'm sure you can think of something in a pinch. I'd probably call it something to do with factions and politics and reading the political currents, maybe even knowing who's who. I know that doesn't sound much like 'Nature' but it is, given a level of abstraction, the Nature of a city, the beating heart that drives it's growth and decay. Anyway, the point is that there are lots of cool options.