Yes she will give birth do an alien sim.
Yes the kid can be put into a disguise.
NO he will not be able to visit his homeland easily you will have to do like any other sim would.
No it shouldnt affect the gameplay exept that that sim will have baby aliens too. It is also possible to breed out an alien after many generations.
Half aliens are called hybrids. For more info on hybrids got to http://www.carls-sims-4-guide.com/lifestates/aliens.php
Here is what my hybrid sim looks like. http://i.imgur.com/IP0cmDT.png