I can relate to your concern. I had the same problem when I lived with a roommate who felt the need to sleep while I felt the need to practice. Now I live alone so I can play as loud as I want whenever I want.
Sounds like you've tamed the majority of sound by playing through headphones. If you are using a solid body guitar, that is about as quiet as you can get your guitar to be without changing to lighter strings which you probably do not want to do unless you happen to have an extra guitar just for midnight practicing.
The only other thing to try is extremely thin picks. Dunlop makes a nylon pick that is only .38mm (paper thin) and will generate much less volume no matter how hard you try to strum. It won't feel the same as heavier picks but just for strumming and practicing chord changes it should be fine. You might find them at your local music store and I know you can find them on line (no more expensive than any other standard pick). I would try to buy just a couple locally to try them before you buy an entire dozen. I would never try to perform with one of those but I do keep a few handy for just the reason you describe - quiet practice (in case I have a guest sleeping over).
You can also find felt picks for ukuleles that are quiet - but they are quite stiff and the alterations you would need to make in the flexing of your wrist to strum with such a pick would be awkward at best and might have an unintended bad influence on your regular strumming movement.
Beyond that, try to find a place in your abode that is most isolated sound wise from whomever might be needing sleep while you are needing practice.
Locate that spot, then orient yourself so the guitar is facing away from sleeping ears and perhaps hang some type of sound absorbing (verses reflecting) soft material on the wall in front of you. Blankets, quilts or acoustic foam or any type of foam padding (yoga mat) that you have handy. You can try securing it to the wall with blue painters tape or a few thumbtacks. Or if you can set up facing a window, heavy curtains would also help absorb some of the sound. Or even sit on the floor behind a couch or sofa - maybe even drape a blanket over the back of a chair and set some pillows or sofa cushions in the chair.
Good luck finding a happy compromise which allows for guitar practice after bedtime. You can never get too much practice on your instrument - but of course sufficient sleep is always a good thing too.