For mods that haven't specified EMC values for certain items, perhaps you could read in the crafting recipe and automatically resolve its EMC value based on the items involved in the recipe?

But what if the base components of the recipe also don't have an EMC value?

This is exactly what's happening. Machine recipes are not working (yet) and recipes with NBTTagged itemstacks are buggy (e.g. batteries). Only IC2 world gen items have been added on top of the vanilla ones. The hard part is finished, the mod integration will come later.