I had a look through it and for the life of me can't figure out what's going on, sorry.

They are not a render type zero; is that related?

That really shouldn't be the case, but you can have a look at the respective code here if you want.
https://github.com/Vazkii/Botania/blob/master/src/main/java/vazkii/botania/common/item/equipment/tool/ItemTerraPick.java
https://github.com/Vazkii/Botania/blob/master/src/main/java/vazkii/botania/common/item/equipment/tool/ToolCommons.java

Found it.
https://github.com/ReikaKalseki/DragonAPI/blob/master/Base/BlockTieredResource.java#L79

I put that there to prevent the normal harvesting algorithm from running (and to prevent most mining machines from dumbly picking up the resources well before a player could have access to it).

If you want, it can be fixed by adding some DragonAPI compatibility, the simplest of which is a simple (b instanceof BlockTieredResource || player.canHarvest()), though that is likely ugly and does not avoid a class dependency unless you have special interface handling.