No, I haven't seen the aqua stones show up as a prize from clearing an Aqua Shadow stage yet. It turns out that the new Seedy Seeds can show up after clearing normal EX Aqua Shadow stages though as well as after clearing EX Destruction stages. Since that's the case and since skip tickets can be used on normal EX stages it ends up being much easier to fish for crystals.

That extremely poor conversion rate is still a serious drawback though.