Transfer missing apps and data to new iPhone

Apps do not transfer from phone to phone. The app placeholders draw down fresh copies from App Store. If they are obsolete or incompatible with the latest iOS then they are totally unavailable to you.

Certainly with Macs some people keep rhe old hardware to use the app, like when Aperture was dropped. You could consider keeping thd SE for those apps

It may also take a few hours for all the apps that are still available to download to the new phone, though it should be automatic.