My curiosity about this topic is because I know a friend of mine who has some brain damage (but can still mostly function in society) due to her mother using drugs during pregnancy. She wants to have kids at some point and I was wondering if the genetic defects that she has would be passed down to her kids. So I'm going to make sure she's aware of this.
Not necessarily. If she has brain damage - either from drug usuage during fetal development by her mother or as a result of hypoxia during birth (lack of oxygen, possibly as a result of delivery), that doesn't mean her eggs are genetically defective, in fact I'd rule it out completely. Her children will be normal as long as are reproductive organs are normal and as long as she has the appropriate number of chromosomes.
In addition, keep in mind that teratogens don't always affect all cells in the body. Take alcohol, for example. It causes brain damage in fetuses due to toxicity. However, these people will have perfectly normal children because their sperm would be normal. It's not affecting the genepool, because the damage is localized, for example in the brain.