Yes, the ray is now subjected to armor since the rules as written are pretty clear and there isn't written anywhere you can make a ranged touch attack. The rules say you can make a ranged attack (so a normal attack with a bow or whatever).
At 2nd level, whenever an eldritch archer casts a spell that calls for a ranged attack, she can deliver the spell through a ranged weapon she wields as part of a ranged attack. Instead of the free ranged attack normally allowed to deliver the spell, an eldritch archer can make one free ranged attack with a ranged weapon (at her highest base attack bonus) as part of casting this spell. The attack does not increase the spell’s range.
Keep in mind that the magus spellstrike (from base class) works the same way
At 2nd level, whenever a magus casts a spell with a range of “touch” from the magus spell list, he can deliver the spell through any weapon he is wielding as part of a melee attack. Instead of the free melee touch attack normally allowed to deliver the spell, a magus can make one free melee attack with his weapon (at his highest base attack bonus) as part of casting this spell.
This ability (spellstrike) never intended to give you a melee touch attack with both your weapon and your spell.
I want to underline that, mechanically, in both cases there is no more a "ray/touch" and an "arrow/sword". There is only an arrow or sword and, if you hit, you can deliver the spell in the same time you deliver the arrow or sword damage.