It is much easier to prevent waste from building up on the bottom of a bare bottomed tank for many reasons...
You can shoot filter returns at the bottom without worrying about stirring up sand...
Since the bottom is flat & smooth currents are not broken up as much thus a little current goes a longer way...
Since there is no substrate for particles to fall between or lock into, waste particles are more likely to be wasted into an intake...
When doing tank maintenance, there is no concern for suckign up sand/gravel so it is faster/easier to siphon off the bottom...
The main reason we use substrate, is because we like the way it looks...
Some fish "enjoy" digging, but they can live without doing so...
Eartheaters may stress out a bit if they don't have sand to sift, but I think they would learn to live with it as well...
Substrate does increase the "surface area" within the system thus giving bacteria additional options of a place to live, but it is exceptionally rare for a system to not have enough "surface area" for bacteria to live... some leads suggest it is implossible to not have enough surface area...