I have noticed that some creatures in the bestiary have a second number along side their toughness. IE: Toughness: 9 (2). What is the second number from? Armor? Size Modifier?
The number before the brackets represents the total Toughness including any protection given by armour. The number in brackets is the proportion of this given by the armour alone.
This often comes into play where damaging attacks include an AP or armour piercing value. If an attack does, you subtract the AP from the armour part of the Toughness before calculating whether the damage Shakes or Wounds the target.
A target lists its Toughness as 8(3).
A baseball bat does 7 damage. As it has no AP, it is compared to a Toughness of 8 and has no effect on the target.
A low calibre pistol (AP 1) also does 7 damage. This time you take the AP from the Toughness giving 7. As the damage equals this, the target is Shaken.
A high calibre rifle (AP 4) does the same damage. In this case though, you only subtract 3 and not 4 from the Toughness, as that is the total amount of armour the target has.
Yes, this indicates how much of the Toughness is due to armour, so that weapons and spells that do AP damage can be calculated correctly.
In the various Savage Worlds bestiaries, the convention is to show the overall toughness followed by the portion of the toughness that is granted by armor. This convention allows you to quickly determine how much of the toughness value can be overcome by armor piercing weapons. In cases where the creature or NPC has more than one type of armor, such as plate on the torso (+3) and chain on the arms (+2), the armor value listed in the stat block is the torso or default value (all hits are assumed to be torso unless the attacker is making a called shot).
All other modifiers such as those granted by Size or edges like Brawny are included in the overall Toughness value. Therefore, if you read a monster or NPC description you can usually assume that any special abilities that would affect Toughness are already included in the stated Toughness value in the stat block.
For a worked example, deconstruct the Orc Chieftain on page 139 of Savage Worlds Deluxe. Toughness is 2 + 1/2 Vigor therefore the Orc Chieftain starts with "7" [2 + (Vigor 10 / 2)]. We look at his Special Abilities and see that he is Size+1 which means his "natural" Toughness is now 8 [2 + (Vigor 10 / 2) + 1]. Now let's put some armor on him. The orc's torso armor is +3 (plate) giving us a total of 11 [2 + (Vigor 10 / 2) + 1 + 3].
We know that the overall toughness including armor is 11. We know that his armor is 3 so we express his toughness value as 11(3). Note that he wears chainmail (+2 armor) on his arms arms and legs which means if an attacker targets those locations with a called shot, the orc chieftain's Toughness would only be 10(2).