Which again is relevant to waterworld or other liquid downports.Yes and if you look at their main holds the are often less than half full volume-wise. Well sealed hatch covers are also standard, as the bulk of the cargo lays at or below the water line.... Draft is often the limiting size to how big they can be.
So assuming you are not going to just ignore all this and further assuming you are going with mostly volume but extreme mass counts, reasonable use cases for mass being an issue is
* flotation/buoyancy on surface liquids,
* extreme density loads,
* mitigation of heavy loads from violent shifting and consequences of same if not mitigated,
* greater limits on higher gravity worlds, and
* heavier capacity when lifting from low gravity worlds.
I wouldn’t seek to have rules that impact all shipping, more like 10-15% of the time when I want it as a plot element.
I would tend to make it more an issue about planetary gravity fields and only a space borne issue at extremes.
That begs the question, do lighter/empty ships around low grav planets ‘go faster’?