In some cases, I feel like they can tell.
My 3rd son has HORRID tooth decay. He's all fixed now, but it took 10+ dentist visits, fillings, pulled teeth, a spacer, etc. to get it all taken care of.
However, the cause of his was being on fentanyl, versed, and methadone when he was 3 1/2. We were hit by a drunk driver. He had impact seizures, a traumatic injury to his brainstem, and had to learn how to walk/talk/eat again. It was a very long process, and two brain surgeries... and because of all this, he was on these medications, along with propanolol and others. The dentist told me that because his decay was from the inside out, it's likely that they started to decay while the teeth were in fact still inside of his gums, when he was 3-4 years old.
Thank goodness we got it all taken care of at the right time, and all of his adult teeth are great now, but those teeth that hadn't come in yet at the time of the accident, were in horrid shape when they finally did pop through.
Not sure if there is a way to tell this with cleft pallet or anything, but I just thought it was interesting to note that sometimes they CAN tell, evidently.