If the game is part of a series or potential series, they would not delete them. If it's a one off, they definitely deleted a lot of assets. A lot of backgrounds, models, and assets from PSOne Final Fantasy games do not exist anymore, for example. This is why a lot of companies that remaster games for HD actually "reverse engineer" the game disc.

Yeah, they do this for PC games as well.

A good example is the Steam release of Final Fantasy VII - it actually ships the original binaries from the 90's PC version mostly intact. Code for things like the Direct3D 6 and software renderers, and MIDI sound is still there in the binary, just unused. All the new features like cloud saves, achievements, and original music are implemented using a separate DLL that hooks a lot of stuff in the game, like the graphics and audio subsystems. It's a pretty fascinating thing to reverse engineer.

That must've been an interesting job :)

Back in the day, I remember using Glide wrappers to run the UltraHLE emulator on non-3DFX hardware. Now, a lot of older games need a DirectX shim to fix various issues (palette and some kinds of slowdowns, especially).