Disney does automatically charge 18% tip on groups of 6+, but it's hard to know if kids under 3 count toward that total since they often don't order their own meals.
The answer as to whether they count toward the 6 is not very definitive, because this policy is not enforced consistently throughout Disney World. So the answer to the question is "sometimes."
You could always talk to your server at the beginning of the meal to find out how they plan to do it. If you feel that your little one shouldn't count, you could try to request that up front, though there's no guarantee on how they'll end up handling it.
Be sure to learn everything you need to know about tipping at Disney World before your trip so you will come prepared.