Attack speed synergizes well with many junglers, who often have on hit procs and red buff. They are strong for ganks and in the jungle. Clearing fast means more experience, less damage taken on each wave, and more opportunities to gank and counter jungle. Ganking is important but the whole point of having a jungler is to take advantage of the gold/exp in the jungle. Maximizing the potential gold available to you is super important when games can be so close.
Not running attack speed runes on Naut would just be dumb. It's too good with his shield and passive.It depends on the jungler. For someone like warwick he sucks at ganking pre 6 so you have to hit 6 asap. For someone like Naut it's not as important because you can gank well and get exp and gold that way.