Whenever my elders said "I think not!" they were very definitely refusing me permission to do or say something.
"I don't think so." could either mean that the speaker did not entirely agree with whoever they were talking to, or could be used by an adult speaking to a child in the sense of "We'll see." an infuriating phrase that children of my generation rightly took to me an "No."
But strictly speaking, "I don't think so." implies that you do not think that whatever was said was correct, but you do no definitely know that it was incorrect, whereas "I think not." used in the sense OP's mother did, infers that she knew for a fact that the expression opinion was wrong.
I suspect, but have no proof, that there may be a difference between Scottish and English use of these two expressions.