They should be hidden as they are truly unique crystals and NOT regular resources! No road signs, neon lights or road maps... They ARE "Game Ending" elements!!!
Funny thing about amazingly important and unique things in real life - you tend to note where they are. Unlike, apparently, my ship captains, who look at an Ascension Crystal, say "Golly gee, there's the amazingly powerful crystal that will let our entire species ascend to a higher plane of existence as beings of pure energy. I guess I'll just drive on by to check out that class zero planet over there, noting it in exhaustive detail in my charts.
Nobody is asking for the crystals to show up before you find them, but it's asinine to not have them show up on your map *AFTER* you discover them. I still have to turn off display of most map elements just to find my own starbases half the time, and I *BUILT* them. Luckily, they show up on my minimap so I can actually find them again. Just having to randomly scroll around an area I've explored already hoping I stumble across where that Ascension Crystal I found in my initial explorations has gotten to is idiotic.
If it doesn't move, it should stay visible on the minimap and through the fog of war once it's been discovered. I refuse to believe that the ruler of an interstellar empire would allow somebody too stupid to mark down an important location on his star charts as captain of a hideously expensive starship.