I'm no liner pond person but I think every thing would be fine as long as you don't have any fish that like to dig and stir up mud. As far as changing water is concerned if you use very low nutrient soil, subsoil actually. You will be adding almost no nutrients to the system, just inert minerals like clay, sand, etc. so they're should be no more need for water changes than without it.
I can imagine that come lily thining time the water would become muddy for a few days from the digging of plants etc. Also you would HAVE to get in the water to do the work. Which is what I do all of the time, but others might not like that.
I know a person who says that he has a 4.500 gal pond with waterfall, stream,etc. He has small rocks and gravel covering the bottom of the pond on top of the liner with no soil. He plants his lilies under the rocks and gravel and he says that his lilies do great with just the mulm he lets accumulate in the gravel and rocks. He says this while standing next to my pond full of lilies so I know that he knows what " doing great " means.