Without reviewing the scans it is difficult to make assumptions. You are
correctCorrect (new formula) that most pineal cysts are found incidentally and are not related to the patient's symptoms. This cyst is small, but in the report is pushing mildly against the brainstem. The only nerve to the eye (4th cranial nerve) which comes out of the brainstem near this region, is lower, and therfore should not be affected by this cyst. However, you should ask the surgeon about this, since he/she will have the opportunity to review the scan.
Regarding the narrowing of the aqueduct, you are correct this does connect the 3rd and 4th ventricles. If the flow of spinal fluid is obstructed/decreased, this could cause symptoms of increased intracranial pressure. These are headaches, vomiting, blurry vision, gait problems, and eventually bowel/bladder problems. However, it seems your daughter does not have these. Therefore the narrowing of the canal may not be significant.
Unfortunately without reviewing the scans I can not be more specific. I hope this helps, and good luck.