They just sit there... Festering...Forever. Looking at your GH's treasury is painful for everyone involved, especially with the worth of the materials going through the roof. For example, my GH has 261 reaper ribs, 140 flame souls, 5 knightmare manes, and hundreds of other 5* mats. Problem is, even the founder of the guild can't remove it from the treasury. Rage inducing. Steam is coming out of my ears right now, it is just far too annoying to look at.
Guildhall treasuries shouldn't be able to accept mats, and the founder should at least be able to take them out and put them where they belong, which is definitely in one of the ranks of storage.
Well, while mats can be used to make boss statues, this is only in later levels. This isn't very good, imo.
I think that they need to enable officers and GMs to sell these mats to NPCs if they cannot be used. That way atleast your guild would have tons of crowns instead, albeit much less than if they were sold via the AH.