I'm not sure they actually will unfortunately, as there technically (from their perspective) is no point. The stone itself is never involved in crafting, never required as an ingredient on the infusion alter, and should never have an 'ore dictionary equivalent' from another mod. This gives them little to no motivation to make Ore Dictionary definitions for them.
The work around I have figured, in regards to mining Infused Stone with the Digital Miner, involves using the custom XML file for the SAG Mill from Ender IO.
Make a custom addition to your SAG Mill XML file, requiring 9 of a specific shard type to create 1 ore block of the equivalent type. You can add these to the XML file using straight item id#'s, bypassing oredict requirements all together. This means that you would only need to collect 9 shards of every type, then you could have a block of each shard type and use it for your Digital Miner filters. It also means you could use the blocks for decor if you wanted to.
That's the best work-around method I can think of.