Counselors, medical providers, teachers, and in some cases clergy are mandatory reporters of sexual abuse under the law. If they know the abuse occured they are required by law to report it to law enforcement not CPS. Now, whether the authorities will act on something that happened three years ago no one can predict.
"If so, what would the ramifications be for my son, or even us, since it was never reported before."
Possible criminal charges for your son. You are not required to report it as parents.
"If CPS is involved, is my daughter required to reveal any info to them?"
No. She isn't required to speak to anyone. That is her choice. She is the victim.
"Would my son, who is now 18 and in college be required to speak against himself? In other words, is a CPS investigation normally a criminal investigation or does it differ."
A CPS investigation can be part of a criminal investigation and can be separate to determine if the home environment is safe. Your son can be questioned and has his Miranda rights. He would be wise to seek an attorney if they do want to question him as any statement he makes can and will be used against him. The cops aren't his friends.
"We kept it in the family since then and there has never been any other incidents or problems with his behaviour. "
That you know of. They typically don't do it once they just get better at covering up their behavior. Your biggest mistake was "keeping it in the family" and covering it up. You sent the worst message in the world to your daughter by keeping silent and doing nothing. You told her it was her fault and she was to blame. The last thing in the world a molestation victim needs to hear.
"But it has been bothering my daughter, and she recently told her youth minister and he recommended counseling. She has told us she wants to speak to a counselor about this."
You didn't put her in counseling immediately? You didn't do the same for him? You just went with a "nobody say a word about this and it never happened" attitude? The fact that you covered it up for three years the authorities just might bring criminal charges.
Why are you protecting a child molester?