It sounds like all the apps use one shiny server and one set of dependencies. So if the dependencies are updated it is expected that some of the apps might break and someone would need to go through them all and fix them. Doesn’t seem like a great architecture long term.
I know Lee has set up a new server using the Shiny Proxy application that provides isolation between apps using Docker. I tested it out and it looked great. So I think that is in the works. I’m not sure what the timeline is for depot the new shiny deploy.