The App Store app update will update the app itself not the data within. For example, you may be able to keep the jepp app up to date, but your charts won’t be updated.
We have different apps, each must be manually updated. Just tap the screen. The only “drawback” is that the iPad doesn’t do multitasking very well, so once you start the update, you have to stay in the app for it to finish. I don’t know of a way to update data in 2 apps simultaneously.
edit- I suppose you could attempt simultaneous updates in split screen mode on the iPad if you have the latest OS.