No, the nomad is not waterproof... but with a coating of marine resin on the bottom side and a good treatment with camp-dry on the top, you won't discover that unless you ride through a lake. One issue with waterproof bags on the BOB is in continuous wet weather, you can get some settled water on the bag near the opening. It gets in unless you are careful to dry the exterior before you open it.
It is still a good idea to keep items which MUST stay dry in actual dry-sacks regardless of how "waterproof" your trailer is. I like the OR and Seal Line bags both for different reasons.
Absolutely no issues with durability on the Nomad. Loctite 242 is your friend during assembly.
The nomad does not track the same way as a kid trailer. The track is narrower, and it is much easier to pull. BOB might as well be an extension of the bike, and is even easier to pull... depending on your BB height and how symmetrically you can load it, there might be a little side-to-side wobble to get used to. No big deal.