Top-tier tools are being broken in the EnderIO farming station. This has been reported on the EnderIO issue tracker as well and marked as not their problem. Perhaps overriding the durability methods on the superium tools would fix this on your end?

EnderIO calls the damageItem methods.

Mod versions:
EnderCore 0.4.1.65-beta
EnderIO 3.1.164
Mystical Agriculture 1.3.9

Forge 12.18.3.2185

http://prntscr.com/e0dh39 looks fine to me.

Also worth noting that Supremium is the top tier, not Superium.