Yes, Montmorillonite clay substrates are safe for the fish. I use Montmorillonite clay in all of my aquariums (75, 45, 30,20,10) with good results. I keep Cardinal tetras, various Apistogrammas, German Blue Rams, various rainbowfish species, rasboras, corydoras, and other species with no issues.
Montmorillonite clay is a calcined (fired/heat treated) clay so it becomes hardened. Not all calcined Montmorilloniteclay is fired the same way and if not fired long enough breaks down into 'mud' in short order. I have used Soilmaster Select, Turface Pro-League Grey, and most recently Safe-t-sorb #7941. The Safe-t-sorb is the most recent type I have tried and it has held up over 3 years now and still going strong with no evidence of 'breaking down'.
Yes, when it is new before it has become saturated with minerals from the water, the high cation exchange capacity (CEC) strips the minerals including the carbonates from the water which in turn lowers the dKH (and PH) a well as the dGH of the water. After the substrate has absorbed as much minerals as it can it no longer has an effect on dKH/PH and is basically inert.
The hydroton/aquaponic clay I have seen is in "balls", it may or may not have added fertilizers. Montmorillonite clay is just fractured calcined clay which contains all of the mineral nutrients of clay and the high CEC properties. You will find several threads about Montmorillonite clay substrates on the planted aquarium forums
Questions, just ask.
10 gallon; Safe-t-sorb #7941 substrate (40# $6.49@Tractor Supply Co); no CO2; low light; set up 10 weeks
30 gallon, set up with Soilmaster Select Charcoal since January 2010, still going strong
As a side note high CEC substrates are not new, I have references to using clay substrates as far back as 1997. If someone is serious about having a planted aquarium with healthy, vibrant plants they should be aware of how the cation exchange capacity of substrate can enhance the growth of plants. As a side note, ADA Amazonia aquasoil is also a substrate with a relatively high CEC; Montmorillonite clay substrates provide a less expensive alternative with a higher CEC. I have heard that ADA Amazonia is actually calcined rice patty soil but I have been unable to verify that as fact.
I have not tried it for aquaponics, just in aquariums. I do use it as a 'capping' material over Miracle-Gro Potting Mix for some of the emersed aquarium plants that I grow. I honestly do not know about mixing two materials, I only use the Montmorillonite clay by itself. That said, the clay is much lighter than gravel, even if you could successfully mix it with gravel eventually the clay would work its way to the top and the gravel to the bottom.
First of all remember that this is a clay product and although calcined (fired) to make it hard it is still clay. I do a couple of things to minimize the cloudiness when I use STS the first time. First I screen the STS through 1/8" hardware cloth. That removes most of the dust and 'fines' but it also results in a loss of about 50% of the bag volume. Then I rinse the STS about six times, put it into my empty tank and do the slopes and grading I think I will want. lay down some wax paper and a dinner plate so when adding water I don't disturb the substrate, finally I fill. I have done both pre-charged and non-charged setups this way. I pre-charge typically with baking soda (NaHCO3) and GH Booster which contains potassium (K2SO4), calcium (CaSO4), and magnesium (MgSO4).
I had already laid the whole substrate before I understood there was too much fine grains. I took out the whole thing apart, did sieve wash which almost fixed it. When I added to the tank, the water again got cloudy. After couple hours with HOB filter, it cleared. But, when I disturb the substrate, the water goes back to cloudy. Is this normal? Does this happen for you?
On my 10 gallon with an HOB filter it did get a little cloudy when I moved plants around for a few months, after that it seemed to stop. Likely the filter had removed the last of the dusty particles by then.