In the context of the gardening / food cycle, space toilets (STs) make would make a lot of sense - the law of conservation of mass will presumably still apply in the future.
In late 20th century/ early 21st century space travel, STs are an important and often under-appreciated part of mission critical hardware; malfunctions have considerable consequences for the crew. Sadly, STs are usually absent from Sci Fi - with the notable exception of the Mass Effect series of games.
Some ideas regarding the details:
1) STs could produce some small amount of mass at each use (presumably they're linked to the matter refinery). This amount could be equal to the mass used by food dispensers minus the mass of packaging (which I assume janitors, when implemented, will recycle). Alternatively, STs could instead produce a new resource, fertilizer, which could be used to grow plants. This would not even have to be explicitly represented, gardeners could just go to the space bathroom to pick it up before tending to plants (it would never fill up or run out).
2) All residents who eat would need to use a ST at some point, probably within a certain random time period after eating at the bar. Not being able to find an unoccupied ST in space bathroom could lead to a decrease in moral, maybe also in health.
3) STs might require maintenance by a janitor (once implemented) in addition to a technician; if not sufficiently cleaned, STs might become a place where users could catch an exciting space disease.
4) A sufficient number of STs might help if there's an outbreak of space gastrointestinal distress (e.g. due to bad food prep by an unskilled bar keeper or mutant plants). Additionally, if any interaction between species and particular meals is planned, STs might play a role in mitigating the fallout of an unfortunate species/meal pairing.
5) Users with different levels of neatness might leave the ST in different states with regard to need for cleaning; different levels of neatness could interact with a given level of ST cleanliness to lower moral more or less.
6) STs might necessitate the creation of a space bathroom zone (although instead of this, maybe STs would be placed in residential areas, prison-style, possibly with a moral penalty if too close to a bed?)
7) Space bathrooms, if implemented, could be a starting point for future expansions: they could also contain space washbasins (decrease probability of disease spread; could cause minor flooding: requires janitor), space showers (boost moral and decrease probability of disease spread; could cause major flooding, damaging objects in the flood zone) and space mirrors (boost to moral / decrease in moral depending on personality)
8) Keeping it (relatively) tasteful: STs could be enclosed in 1x2 stalls that close when occupied / glass stalls (so players can see the awesome looking ST) that turn opaque when in use.
9) Impact (reiterates the points above):
a) Duties: technicians, janitors (when implemented), gardeners (when implemented and if STs produce fertilizer)
b) Behaviors: everybody uses a ST some time after consuming a food item
c) Moral/Health: moral/health lowered if no ST available; moral/health lowered if ST improperly maintained; point of disease origin if improperly maintained; relief from certain diseases / food incompatibility events
d) Base construction: potential new zone (space bathroom); new item for zoning size calculations when building a room
e) Resource chain: either produces mass (proportional to mass used at food dispenser) or fertilizer (used to grow plants for food)
10) Yes, I'm aware I just spent considerable time writing about virtual toilets in space.