I know a lot of us have a slight hope that would have been used for some sort of relic weapon, but that probably isn't happening with Jobs and 2.0 coming (too much is going to change), but why not think of some practical uses and hope that someone pays attention to this thread?
My first idea is to exchange them for keys in the strongholds. Chests have 3 tiers and currency has 3 tiers. Why not exchange 100 Ixali Willowknots for a Bronze Key? Maybe 60 Mapleknots for Steel and 40 Ebonknots for a Gold. Reaching the chests is still a challenge and carrying only one a time would force you to run the gauntlet, still forcing you to make some effort.
Post your ideas.