ST4 creates a folder for each song, and copies the assets (tracks, MIDI file, etc.) into that folder.
There is no 'sharing' of assets between songs. If you have a common MIDI file you are adding to multiple songs, then a copy of that file will be in each song folder. Therefore, deleting it from one song has no absolute impact.
Just in case this is something you are doing, as a general rule of thumb it is not recommended to manually manipulate the Stage Traxx 4 folder on your iPad, and that includes using it as a source for adding/reusing assets. It is recommended you always add tracks, MIDI, lyrics, etc. from outside of this folder structure and let ST4 manage its folders and their contents.