Is there a good way to run android apps on desktop?

Windows Subsystem for Android.

Or is it Android Subsystem for Windows?

Android apps appear to run natively on Windows (so they're not in a VM looking box, they behave like Windows apps). They don't have access to the local file system, they have access to their own file system, just like using a phone.

The easiest way to move files in/out is to use a file manager that can access SMB shares (like MiXplorer), or use Syncthing on the desktop and in the Subsystem, and sync a folder on the desktop.

Some people have gotten Waydroid to work for this, not me though

It's Waydroid. Since your current setup doesn't have Wayland, you could always try setting up a VM with a distro that has Wayland or even Waydroid already installed like VanillaOS.

Can confirm waydroid works fine.

Also i dont know what its running under the hood, but i just installed minecraft bedrock launcher flatpak on my steamdeck. Which runs the android version.

Waydroid can be sorta annoying to set up, id suggest not taking any shortcuts and install the base waydroid package then following the instructions on archwiki or whatever to manually install the appropriate container (gapps etc) rather than using the container package from your distro.

I havent set this up in probably over a year so between my foggy memory and potential changes, take this as you will