I had this same issue, but was able to find a workaround.
The dsi cfw guide to autobooting dsimenu++ states to make /shared1/TWLCFG1.dat and /shared1/TWLCFG0.dat read only, change them back to read/write, disable autoboot title, edit your settings, then change them back, you can have wireless disabled. This also applies to profile, date, and time settings.
Additionally, if you are unable to access system settings inside dsimenu++, edit the file /_nds/dsimenuplusplus/dsiware/System Settings (U).argv to point at the correct .app file in /title/00030015/484e4245/content/, assuming your DSi is US region.