my 3 yr old is autistic. does this mean i check the "was disabled" box on his info page?

No, that won't apply since the child in not age 18, you won't get any additional benefit by checking that box.

Do I get a credit or deduction if my child is disabled?

If your child is older than 12 and you need to pay someone to take care of him while you work, you can say he is disabled and you can still get the childcare credit on your federal return.   Or if he is 19 or older you may still be able to claim him as a qualifying child dependent on your federal return.

Aside from those things, there is no federal tax advantage to saying that your child is disabled.   Your state tax laws might be different.