On my 5,1 running Mojave, I will get notifications that updates are available, but when I click update, they just hang on trying to update. This has been going on for several weeks. No problem with my other Macs.
You are correct, the OS updates do, but regular apps still update throught the App store in Mojave. It is not working on my 5,1, but does on my rMBP, both on Mojave.