Does a horse have two natural attacks (bit, hoof) or three natural attacks (1 bite, 2 hoofs)? Also, are the hoof attacks considered secondary if the animal companion is trained for combat, or are they considered primary, like normal combat-trained horses?
Relevant Rules (natural attacks will be parsed for illustration purposes)
Docile (Ex) Unless specifically trained for combat (see the Handle Animal skill, a horse's hooves are treated as secondary attacks.
Natural AttacksMost creatures possess one or more natural attacks (attacks made without a weapon).
These attacks fall into one of two categories, primary and secondary attacks.
Primary attacks are made using the creature's full base attack bonus and add the creature's full Strength bonus on damage rolls. Secondary attacks are made using the creature's base attack bonus –5 and add only 1/2 the creature's Strength bonus on damage rolls.
1. If a creature has only one natural attack, it is always made using the creature's full base attack bonus and adds 1-1/2 the creature's Strength bonus on damage rolls. This increase does not apply if the creature has multiple attacks but only takes one.
2. If a creature has only one type of attack, but has multiple attacks per round, that attack is treated as a primary attack, regardless of its type.
3. Table: Natural Attacks by Size lists some of the most common types of natural attacks and their classifications.
Natural Attack ... ... Attack Type
Hoof, Tentacle, Wing ... Secondary
1. The context of "attacks" almost always refers to 'attacks' rather than 'weapons'.I am fairly confident that this means your horse has 3 attacks.
2. The Docile SQ of the base horse is what overrides this rule.
A standard wartrained mount uses this rule because it is not longer docile.
3. However, your AC no longer uses #2 because it now has more than one type of attack, forcing the hoofs to default back to secondary as per the table.
I hope this was helpful.