1. Make rune combinations dependent on correct order of the runes. This should be easy to implement and prevents the player from finding out combinations too easily. I remember a 1992 RPG game The Summoning where you incidentally also had runes but for spells you used hand gesture combinations like runes in your game and they were majorly correct-order dependent. This will also allow you to use a certain rune twice in the same spell which makes the combinations longer and allows for many more spells and effects without adding more runes.
2. Add curses aka permanent effect ill-causing spells which result from improper runes combinations. Can also be random from various improper runes combinations. Like base strength -1, summon a strong monster, darkness curse, schizophrenia curse (monsters which are not really there), etc. This will either make determined players to reload a savegame to find out all combos or prevent the undetermined players from messing with the runeboards. Read the next point why this is important..
3. Make information about runes combinations for most spells available in-game via merchants, NPC encounters, random plaques, etc. You may also make the combination revealed within a text-only description which is incomplete (as in "I have split this scroll with my brother, because the spell it contains is way too powerful to use by one person. I hope I reunite with him when he comes back and we will use this spell to make things right. The Spell of Waymaking is made by using following runes in this very order: Aard, Heth, Tau,.. [the rest of the message was unfortunately torn away]"), which would encourage players to try some new runes combos. Or make custom messages with riddles containing the spells (the runes combination would be encoded in the caps of the text, etc..).
4. Make some special spells and information about them accessible via different routes. One route could be an app notification. Another could be a forum message. Another on a partner website
