There are thickened Epoxy Resins that work excellent for bonding, sealing, and filleting the plywood seams. I've used Max Bond Thixotropic for this purpose. One of the main advantages of epoxy resins, such as Max Bond Thixotropic, is that it has a long tooling or work time, which is about 90 minutes before it starts to cure.
The main problem with silicone is that the outer layer skins over after 5 - 10 minutes after you apply it, which greatly affects it's tooling and adhesion ability. When plywood tanks with silicone seams leak or fail, the 1st problem I think of is that they probably tried to work too much of an area at once before adhering or smoothing the silicone. They may have caulked multiple tubes of silicone, which took them 10+ minutes, so the silicone skinned over, and didn't adhere well. Or they they used more than one continuous bead of silicone, so when they attached the panel, the air pocket between the beads caused much of the silicone to squeeze out, leaving multiple air gaps. You need to work quickly with silicone to achieve it's maximum adhesion ability. With large complex plywood builds, sometimes one person just can't work fast enough to use silicone. It may take multiple people to do the job properly in such a small time frame.
Silicone seams could work fine in a plywood build, but you just need to know it's limitations. You may not want to epoxy over silicone fillets in the corners because silicone is a very soft and weak to use as a substrate. In a small tank it probably won't matter, but in a large tank it might. If you fiberglass the seams, it probably won't matter either way. You certainly can silicone over the epoxy though, which is needed for adding the glass panels.
To get an idea of just how soft and weak silicone is compared to Epoxy resin:
Hardness of Silicone: 17 Shore A Scale
Hardness of Epoxy : 75 - 85 Shore D Scale
Tensile Strength of Silicone: 195 PSI
Tensile Strength of Epoxy: 3,440 - 7,846 PSI
For attaching glass panels, silicone is still the best product to use because it is UV resistant, moisture resistant, and very flexible. Epoxy resin is not UV resistant or flexible.
Sources:
http://www.smooth-on.com/Durometer-Shore-Ha/c1370/index.html
http://www.siliconeconcepts.com/pdf/WeatherSealants/GP.pdf
http://www.westsystem.com/ss/typical-physical-properties/
http://www.glassonweb.com/articles/article/769/
