Yes, permanent transformations will happen at the end of an individual character's story arc. So it won't be happening anytime soon for most characters, but it's definitely in the plans eventually. At the very least, you'll 100% have epilogues that take all of that stuff into account. Epilogues are what I live for. Mass Effect 3 broke my heart when it first came out lol.
And yes, you'll be able to not only impregnate everyone, but also customize whether they know or not that it was you who impregnated them. The sister impregnation scene I mentioned above is one that will allow you to later (not yet implemented) have sex and tease her with the fact that she's such a slut she has no idea who the father is -- even though you know it's you lol.