You really have nothing to lose by trying one or two pots of waterlilies at a deeper level. You could try one and see how it goes for you.
All my waterlilies are not at the recommended 18-24". A number of years ago, we had our waterlily pots on the plastic cubes that the college kids buy to hold files. The general idea at the time was to put the waterlilies at the recommended growing height. I had a fish that got caught between the plastic cubes. Apparently he had himself wedged in there rather well, because he could not get out until all the pots of waterlilies were removed and the plastic cubes where pulled out of the way. At that point in time, my line of thinking was I didn't really care as much about the waterlilies if it meant my poor koi were being put at risk. So, the cubes came out of the pond and the waterlily pots were put at the very bottom of the shallower end of my pond, which is 3 1/2 feet.
Every year, I get nice pad coverage and my waterlilies flower from spring through to fall. So, give it a try with just one pot of waterlilies and see what happens. Nothing is right or wrong. :wink: