By default, a pickaxe will turn draconium ore to draconium dust. When using the digital miner with Silk Touch, you get the original ore, but the ores cannot be handled by any Mekanism factories, therefore it has to be taken out of the miner and manually mined into dust, before then being put back in the system to let the smelting factory convert that dust to ingots (which does work).

you could have it routed to a block placer/block breaker and then sucked back into the system

That's what I'm considering for now.

Resolution pending integration from #4239.

Doesn't handle Nether Draconium Ore, but that's because that ore (from the same mod) doesn't even have an ore dictionary entry.