Yes, soy affects hormones. My daughter was allergic to milk, and the only thing I was told by a Pediatrician to use was soy for her bottles (I was unable to breastfeed). I am SO UPSET that I didn't know better at the time. I would have used goat milk or something else, ANYTHING but soy. Thank goodness, she didn't have precociousness/early development, which I was very concerned and worried about.
If your child has a milk intolerance, then you need to stop feeding your child everything and anything that has (cow) milk in it. You'll need to read labels; that means anything with caseinate or whey in it, too.
Have you tried giving your child goat or sheep products? Our family cannot have cow products, but we are able to eat goat and sheep. I buy a really good, mild goat cheese from our local co-op and a mild sheep cheese from COSTCO. We all love them. I love goat milk, but no one else in the family really does, so I don't drink goat milk much. I know your 18-month-old is still quite young, but when able, there are lots of milk alternatives, like: rice, almond, hazelnut, hemp, oat, coconut. All of them taste good. We like almond, rice, hazelnut, coconut, in that order.
No matter what age you are, I would strongly encourage most people--especially women--not to fall into the "soy is better" category. No, soy is NOT better for you. In fact, flax seed and chia seed are vastly superior to soy.