Can an abnormal head shape hurt my baby's brain?

See below. It depends on what kind of abnormal head shape. If there is some mild flattening by lying on back, or in one position all the time, then there is probably no affect on the brain. If the abnormality is formed by the skull sutures fusing, so restricting the space inside the skull, then yes the brain can be hurt. Talk to your physician about which problem you are dealing with.
No. There is no clear evidence to support the idea that abnormal head shape due to sleep positon and/or limited neck movement can hurt the developing brain. In children with skull bone banormalities, that is less clear and there may be increased pressure within the head that might interfer with normal brain development. This is why it is important to separate these two conditions.