Missing Software Citations
Reaching out to journal editors might backfire, I'd be careful with that approach.

Ultimately it's going to be up to your users to a) know how to cite your work and b) decide to do so. You have some control over a): you can display a short note with the preferred citation when the program starts. In the case of an R package, you can use the function .onAttach to display a message when your package is loaded. If it's a stand-alone program, put the message in your splash screen, or on the console, wherever a user might see it.

In the short term, you don't have any control over b), so I suggest you focus on maintaining the program and responding to users as best you can. As we use an increasing number of programs, deciding which ones get cited in any given paper is going to be a bit subjective. If my analysis depends on a bug fix or new feature that a developer implemented for me, they will definitely be cited!

Beyond that, your influence is limited to longer-term approaches to changing practices:


lead by example, so people become accustomed to seeing software getting cited
as an editor or reviewer, request citations be added where you think they should be
promote the idea to your students and colleagues