Since the rules are poorly described for touch and ranged touch attacks, should the size modifier apply when making these types of attacks?
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.