I grew up as a RiscOS user, which had this kind of application folder system.
Package management is >much
If you are going to have shared blobs of code like shared-objects/DLL you need package management, end of story.
You want one copy of each, or a least one of each version, and you want to update that one file. Even on modern machines, you don't want to statically link everything, even if you did, think about updates. If one of these files need a fix, it's much easier to update that one file, then update every program built statically against it. Use version number as part of the filename and have a sym link without the version number to the latest version. If something needs a specific version, it can be built to link to that not the latest. You can do as many version levels of this as required. Seriously, this is much better centrally managed and updated. You can even list all applications that use the file, even before anything is installed. I wouldn't go back to an application folder system if you paid me to. Windows has some central management with the manifest stuff and add/remove programs, but compared with Debian package management, it's an over-complex mess or a fraction of the power. Other package manager might be as good as Debian's, but so far, none have impressed me as much.