Phil has provides one of the reasons for adopting them below. Looking up Marine Vacuum Toilets should get you other reasons from the advertisers selling them. Where our "geniuses" seem to have screwed this up is by using piping which is too narrow. That actually might have been an attempt to save money...buying something too small.
Honestly, our ship yards are doing lots of crappy work these days. (Pun intended upon afterthought.) Where the Navy would be at fault is in a lack of proper oversight. Shoddy contractors for the government is nothing new. During our Civil War, many food vendors passed barrels of horse meat off as beef. Some government inspectors caught some, others didn't know the difference, and others still were bribed to pass it on. Many of these issues which are popping up these days were preventable with better oversight, but I believe I recall reading that our Navy undid its inspection branch some years back (or reduced its operability level in some way. I am not remembering it in any clear detail.) Here is an opinion piece which I would definitely be in agreement with: