Unfortunately, no. The only emulator on 3DS that supports Super Gameboy color palettes is Gameyob and that's not one of the options in NSUI. The 3DS port of Gameyob actually doesn't support Super Gameboy borders, though, so the best way to play Gameboy games with SGB support on 3DS is still the DS version of Gameyob. There's a DSiWare installer for it.
One thing you can do is inject B&W Gameboy games using the Gameboy Color VC injector so that you get the GBC palettes, though those are usually not as good as SGB palettes. You can also add custom borders to a GBC inject, so you could give the inject one of the original SGB borders that way.