Re: So I've noticed that app.midnightbsd.org is down
The app store isn't discontinued. It might have been going through maintenance that day.
The differences are as follows:
The mports page is the ports tree. That's what is available to build from source. It's always going to have more stuff than the app store page.
The app store is what is available in packages for a given version and architecture. This data is built from the Magus package build cluster based on runs that are marked "blessed". This means they were published as packages for that release. The app store data gets updated based on the latest run that is blessed in magus where magus is located at https://www.midnightbsd.org/magus/
The app store website also populates some data like ratings into the graphical package manager app. The CLI app "mport" does not connect to outside sources except to fetch packages.