Yes, ranged attacks from spells are typically considered to be "weapon-like". This is definitely true of rays (and almost all ranged touch attack spells are rays) since from the rules:
You aim a ray as if using a ranged weapon
The rules further clarify that rays function as weapons for several other purposes, and the FAQ makes this very explicit:
Do rays count as weapons for the purpose of spells and effects that affect weapons?
Yes [...] rays are treated as weapons, whether they're from spells, a monster ability, a class ability, or some other source
The same rule applies to weapon-like spells such as flame blade, mage's sword, and spiritual weapon--effects that affect weapons work on these spells.
Most ranged touch attacks which aren't rays are things like acid splash -- spells where you actually throw or aim a physical object. Those are even more "weapon-like" than rays, so it's probably simplest to say all ranged touch attacks work like this.
There's another FAQ that indicates you can take "Weapon Focus (ray)" and the like; strictly speaking I guess those wouldn't apply to orb spells like acid splash.
This is all following the precedent set by 3.5; in Complete Arcane it specifies that rays and touch attack spells are "weapon-like" and thus interact with feats in the same way that other weapons do, with a split between ranged/melee type spells.
The RAW doesn't specifically say.
As you note in your research, none of the rules related to hitting objects have any information about what to do if the object is attended.
That said, you can use existing rules to figure out a reasonable alternative. The rules for smashing an object that you link say:
An object's Armor Class is equal to 10 + its size modifier (see Table: Size and Armor Class of Objects) + its Dexterity modifier.
If you try to use the spell rusting grasp on someone's armor:
You may employ rusting grasp in combat with a successful melee touch attack. Rusting grasp used in this way instantaneously destroys 1d6 points of AC gained from metal armor (to the maximum amount of protection the armor offers) through corrosion.
You can similarly touch a weapon with rusting grasp:
Weapons in use by an opponent targeted by the spell are more difficult to grasp. You must succeed on a melee touch attack against the weapon. A metal weapon that is hit is destroyed. Striking at an opponent's weapon provokes an attack of opportunity. Also, you must touch the weapon and not the other way around.
It says that weapons are harder to grasp, but it doesn't actually give any rules for how you should determine the AC of the weapon.
With this in mind, one reasonable ruling would be to apply this rule to attacks against attended objects, but let the object use the attending character's Dex bonus instead of its own, as well as any other modifiers that the character has that apply to touch attacks, like deflection bonuses or a monk's Wisdom to AC. If you try to touch an attended weapon, you provoke an attack of opportunity. This means that it's a little bit harder to hit an object that a character is attending than it is to hit the character, since most objects are smaller than their users.
Another reasonable ruling would be to say that it's a Combat Maneuver, like any other. In this case, I'd say that touching an object that's being attended by another creature would work like Sunder. In this case, you'd simply make a CMB check against your opponent's CMD, provoking an AoO if you don't have Improved Sunder. The drawback of this approach is it means that it's basically impossible for casters to touch an object being attended by a creature except at very low levels, since the CMB of a caster goes up very slowly, but the CMD of most other creatures goes up very quickly.
Best Answer
A creature's size modifier on attack rolls usually applies to all of the creature's attacks
Unless exceptions apply, a creature's size modifier on attack rolls applies on all attack rolls that the creature makes, whether the attack is a melee attack, a melee touch attack, a ranged attack, or a ranged touch attack. While Attack Bonus does specify melee weapons (and Touch Spells in Combat on Touch Attacks says, "Touching an opponent with a touch spell is considered to be an armed attack") and ranged weapons, I've never seen a creature's size modifier excluded from its attack roll when the creature uses, for instance, a natural weapon or a ranged touch attack.
(For example, a dark naga possesses a base attack bonus of +7 and a Strength modifier of +2 yet with its bite its attack bonus is, without explanation, +8, but that mysterious additional −1 can be explained by the creature's Large size. Likewise, the azruverda possesses a base attack bonus of +12, a Dexterity modifier of +2, and the feat Weapon Focus (acid), yet with its acid—a ranged touch attack—its attack bonus is +13, the mysterious additional −2 explained neatly by the creature's Huge size.)
Elsewhere—such as on the Table: Size Bonuses and Penalties, in the Advanced Race Guide on Size Quality, and in the description of the transmutation subschool polymorph ("If a polymorph spell causes you to change size, apply the size modifiers appropriately, changing your… attack bonus…")—a creature's size modifier seems to be considered a modifier on attack rolls generally rather than a specific modifier that applies only on attacks made with melee and ranged weapons.
As a creature's size modifier is applied to all its attacks in other parts of the game, I suspect Attack Bonus is written with the typical PC in mind—the typical PC usually making attacks with melee weapons and ranged weapons—, rather than Attack Bonus making a broader statement about how size bonuses function throughout the game.