Can you please post link to configuration of your phone? Native duke port and running duke in emulation are different things. Native port was rewritten and recompiled for modern phones. Emulation depends on strength of your cpu. But thats weird, dos emulation is without issues long time on modern devices.
The game has configuration tool – SETUP.EXE. Try change resolution there. Try set sound blaster 2.0 in game profile and in SETUP.EXE. This should improve performance.