Seems like you don't need to mention other programs either way. Just contact the appropriate person, let them know you're excited to have learned that your SO matched in their city.
I was applying while a non-medical husband was in a nation-wide job search, and I was very upfront with programs about what he was applying for in the city and why it made their program attractive to me. I don't remember ever worrying about doing it with two programs in the same city....