Gus,
if the aeration system is sized properly for the pond, it should not only help stop muck accumulation but help decompose what was there to begin with. aeration experts could help more here.
if the pond is not leaking, you could safely assume you have good clay soils under it, however, anytime you dig deeper, you risk breaking the clay seal......it would help to evaluate how thick the clay might be either through doing a couple test pits, revieweing local water well log information, or having a reputable pond/geo/engineer consultant take a look at yer place....then determine excavation methods if you go that route.
assuming the aeration is doing its job, and if the pond is fishing good though, why do you want to deepen it? what are yer goals?
