Both approaches have the same disadvantages actually. With Joplin Server, it would manage sharing, etc. but it will also need to manage your sync items, so you can’t use it next to Dropbox, Nextcloud or anything - it’s an all or nothing.
With the Nextcloud app, it’s similar, you can only use it with Nextcloud but of course, many more of Joplin users already have Nextcloud so it’s less of an issue. If you already have Nextcloud, it’s also very easy to install - you just press a button and it’s done.
So in the end, it was making more sense to make a Nextcloud app. Also it already handles user authentication, file access, sharing, database and other features needed for this, so it’s also a lot less effort.