The ability Nighteye (Ex) gained at 3rd level states: "At 3rd level, the nightblade gains darkvision out to 30 feet. At 9th level, this distance increases to 60 feet. If the nightblade already has darkvision, its range is increased by these amounts. She also gains Blind-Fight as a bonus feat. If she already has this feat, she can choose any other feat she qualifies for." When exactly does she get Blind-Fight, at 3rd level or at 9th level?

She gets Blind-Fight at 3rd level.

If I take the Path of the Darkened Fortress, I can use Shadow Armament to create a single melee weapon, and Versatile Armament to create dual weapons or a ranged weapon... but neither mention double weapons (quarterstaff, doubleaxe, hookhammer, etc.).

This was an oversight on my part, I didn't consider double weapons. With Shadow Armament by RAW you could make a double weapon, but only one end of the dual weapon would be enhanced. If you want to enhance both ends of a double weapon, you need the Versatile Armament art and should treat it as creating two weapons.

How does the Shadow Barrier ability for the Path of the Darkened Fortress work? Can I use it against a target I can't see? How long does it last?

The barrier lets you gain cover against attacks made by a single opponent. You do not have to be able to see the opponent to use this ability; it works much like a swashbuckler's dodging panache deed in that way. It is supposed to only last until the start of your next turn; if no attack is made during that time, the barrier vanishes. This ability will likely be reworded in future editions to better clarify how it works.

Shadow Armament is a (Sp) spell-like ability and Versatile Armament is a (Su) supernatural ability. Why would attacking with one shadowstuff weapon be subject to spell resistance and dispelling, but attacking with two shadowstuff weapons or one ranged shadowstuff weapon would not?

It's supposed to be an enhancement to Shadow Armament and not a stand-alone ability, in the same way that arts like Piercing Armament (Su) and Bloodied Chains (Su) are meant to enhance their respective path powers. When making two weapons or a ranged weapon treat it as if using Shadow Armament itself (a spell-like ability).