As a result, they're totally useless, so either they should have a nugget to ingot recipe and vice versa, some way to convert them to dust, or be completely unobtainable.

https://github.com/aidancbrady/Mekanism/blob/master/src/main/resources/assets/mekanism/recipes/ingot_3_alt.json
https://github.com/aidancbrady/Mekanism/blob/master/src/main/resources/assets/mekanism/recipes/ingot_0_alt.json

Are you sure you don't have crafttweaker recipes removing these or the oredict entries?