Technically Soma is accruing their souls to summon them via the "command" ability he has as a result of being reincarnated Dracula.
So then, is the demon still inside the crystals which Miriam absorbs? lol, I've got 60+ hours into the game and don't have a straight answer.
If I understand Johannes' description and the archived journal correctly, the shards are an accumulation of energy that can channel and manifest certain powers, not living creatures. This also extends to the familiars, as their respective shards "summon" them from their own realm through Miriam's ability to bind the power of the shards to herself. So no, the crystals don't house the demons, only the powers that they use, which is oddly specific, but that's how it's told.
As for Soma, that's pretty much on point. To be really specific (and semantic), Soma's incomplete "Power of Dominion" (also known as "Soul Steal") can command the souls of monsters, or generally, the souls of chaos (which is why he cannot control or influence human souls, for instance, unless the person is evil/corrupted). However, the souls don't always answer his call, since the power Soma wields is not fully awakened, and he most likely doesn't use it subconciously. Funny enough, that explains why the souls have a drop chance - failure means the soul returns to the heart of chaos, success means it hears the call of its new master.