I trained heavily into spotting all iron/plants/runes since I was stuck in stros m'kai due to server not allowing you to change area's (infinite loading+ disconnect if you tried it), so I know every inch of stros mkai now, and the runes, are VERY easy to miss, I literally saw players pass by them, and I understand why.
If you look them at the angle that only shows the stone part, you will never notice them, but after a while my eye could spot them at a huge distance thanks to the middle light they had.
Also they're usually between rocks most of the time, so every time you see some unusually larger rock combo, a rune is probably put there, also found in "corners" of rocks like a "V" shape.