As has been stated many times, dosbox DS was a proof of concept, a failed attempt, with which it is not possible to play games. The ones that seem to work freeze a little later or are so slow as to be unplayable.
Use this instead, which is far better: very old DOS games work with this: https://dsx86.patrickaalto.com/
yeah, as far as im aware, i opened anemone 3ds theme manager, installed the theme and then deleted it from my sd
and it stayed applied even after i rebooted the system. although I'm not sure for more long-term situations