For the purpose of getting a +3 to an animal companions skills, are skills that an animal companion invests in considered class skills?
The rules as written state the following:
This lists the animal's total skill ranks. Animal companions can assign skill ranks to any skill listed under Animal Skills. If an animal companion increases its Intelligence to 10 or higher, it gains bonus skill ranks as normal. Animal companions with an Intelligence of 3 or higher can purchase ranks in any skill. An animal companion cannot have more ranks in a skill than it has Hit Dice.
Animal companions can have ranks in any of the following skills:
Acrobatics* (Dex), Climb* (Str), Escape Artist (Dex), Fly* (Dex), Intimidate (Cha), Perception* (Wis), Stealth* (Dex), Survival (Wis), and Swim* (Str).
All of the skills marked with an (*) are class skills for animal companions. Animal companions with an Intelligence of 3 or higher can put ranks into any skill.
But unfortunately they don't mention anything about whether or not investing in a skill gives them a +3 rank bonus, similar to how a PC would receive a bonus by placing a rank in a class skill.