Elder Russell M. Nelson gave a great talk about the process of translation at the Missionary Training Center, and he spoke about this process of Joseph figuring out how to translate.
It does seem supernatural, but so are most of the amazing stories in the scriptures–Moses parting the Red Sea, Joshua crossing the River Jordan, marching around Jericho seven times and the walls collapsing, David slaying Goliath, Samson killing 2,000 Philistines, Christ healing people–himself rising from the dead! etc. We come to expect supernatural things from our God and His servants. Joseph’s use of a seer stone or the Urim and Thummim to translate fits in with all the other miracles that have been documented in the scriptures.
The Church’s curriculum department must meet the needs of all members. This means everyone from the just-baptized and uninitiated to the seasoned scholars. It’s a tall order to serve milk to some and meat to others, so what generally happens is everyone mainly gets milk. I think the Church prefers that members who are prepared to get more carnivorous in their pursuit of Church history and deeper doctrines learn it through independent study. But the information is readily available to those who want to know. I searched “seer stone” on lds.org and it came up with a list of links with conference talks, manuals, explanations, scriptural citations and other information.
The Church isn’t trying to hide anything–if it isn’t spoon fed into your mouth each week at church, seek it out on your own through prayer, scripture study and other resources (like lds.org). The Lord will readily teach a searching mind (see Matthew 7:7).