In general, acidic or basic foods are very safe from bacterial contamination standpoint. Soda is very acidic (due to all that dissolved carbon dioxide).
It's not that it doesn't get bacteria (they live everywhere), but it's unlikely to get pathogenic bacteria. This makes sense, a highly acidic environment is very different from a human body.
That's why foods such as milk, ice cream, potato or egg salad, are the most dangerous from the bacterial contamination standpoint.
Soda is not "very acidic", for the exception of coke, which has strong acid added to it. Carbonic acid is very weak, and won't prevent bacteria from growing.
The Wendy's frosty machine doesn't have the same automatic cleaning cycle and pasteurization feature that the McDonald's ice cream machine has. Thus Wendy's employees need to tear the machine down and clean it by hand, a long and tedious process.
The whole reason McDonald's wanted this machine was to reduce training costs and labour. However, the machine does need to be operated correctly or it simply shuts down.
Maybe for you but when closing a Wendys down for the night you need to begin the teardown process quite a bit before official closing time. You need to wait for the machine to allow the remaining frosty mix to melt, dump the remainder into a metal bucket (to use for tomorrow). Then you have to flush water through the machine to be able to disassemble it, then the machine needs to be loaded with a sanitizing solution (along with all the parts which are placed in the hopper).
Finally you gotta re-do all of this the following morning! Sure its not like taking apart an iPhone but its not a 5 second job either.
The worst part? This damn machine can only produce one flavor of frosty at a time! The mcdonalds machine avoids all of this, produces 3-4 flavors of milkshakes from one unit and handles soft serve ice cream!
It's not a self-contained TPN compounder in a hospital cleanroom. It's a machine that has many parts that get wet with sugary water. It has parts that need to be cleaned that seldom are, and judging by the average fast food employee, would probably be better off left alone than further contaminated by them attempting to clean it. Google "soda fountain mold" and you will be stunned to see how nasty these can get. I don't eat fast food often, but I skip the drink unless it's from a meticulously clean place.