The process plants run better on fresh water but fresh water is expensive and heavy on a ship so a vacuum system allows for less water per flush and really works pretty well if people don't flush stupid things.
Stupid things that my co-workers have fished from sewage plant besides the things mentioned in the article: Towels Screwdrivers Glasses Rags baby wipes/ flushable wipes Pens
As long as only body waste and a small amount of toilet paper are used, the systems are actually fairly reliable. Teaching people that that is ALL that can be flushed is an on going problem. The chemicals seem to be another issue, possibly a design issue but there are ways around that too. Urine crystals build up on the walls of the pipes and reduce the diameter for the waste water to flow. The vaccum systems typically have smaller diameter pipes then the old style "gravity" flush systems. There are companies that make continuous dosing systems that go in the end of the branch lines to help keep them clear.
A lot of issues with maintenance can be solved by design of branches in the piping system with isolation valves so the whole system doesn't have to be shut down to fix something. Even replacing a toilet means shutting off the branch or system since it opens a hole in the vacuum system and leads to loss of vacuum.
Some more information: https://www.boatus.org/clean-boating/sewage/msd-types/
Manufacturers: https://jetsgroup.com/jets-group/the-highest-standards/the-h... https://evac.com/
One thing of note: seems the whole system is designed for peace. While I can understand armchair designer (it is likely it will never see something like WWII action) this should be designed as a machine of war in case all hell breaks lose. I guess the backup plan is to have buckets and a bucket brigade...
Having one system for when the ship is out at sea and switching to something else causes even more engineering problems. Even if you're not processing the waste, the vacuum sewage system would still be used to collect the waste to discharge it.
MARPOL Laws: http://www.imo.org/en/about/conventions/listofconventions/pa...
https://www.dco.uscg.mil/Our-Organization/Assistant-Commanda...
Special Sea Areas: http://www.imo.org/en/OurWork/Environment/SpecialAreasUnderM...
For example, suppose that you move part of the "processing" into the mechanism of the toilet itself, i.e. you use some kind of lever-operated press to pass your own output through a sort of a sieve; only soft items will pass, or items you break apart - but then you notice you've broken something apart which demotivates throwing those things in the toilet.
Just a thought.
EDIT: See https://www.navy.mil/submit/display.asp?story_id=103122 for a 2017 press release describing how the Reactor Department produces fresh water aboard the aircraft carrier USS Abraham Lincoln (a Nimitz-class carrier, i.e., an old design). TL;DR: It's done with giant evaporators, that is, distilling units.
Fun fact: At sea, one of the big uses of fresh water aboard a carrier is the repeated washing down of the aircraft to reduce corrosion from the salt air.