Yes but he never respected them. At Auschwitz they went straight to the shower.
Any evidence of this? There was probably only a few thousand Muslims in Germany at the time and I don't believe they were seen as enemies in the Nazi ideolgoy:
Taken from Wiki:
The rise of Nazism in the country did not target Muslims. Adolf Hitler repeatedly expressed the view that Islam would have been much more compatible to the "Germanic races" than "meek" and "feeble" Christianity:
“Had Charles Martel not been victorious at Poitiers [...] then we should in all probability have been converted to Mohammedanism, that cult which glorifies the heroism and which opens up the seventh Heaven to the bold warrior alone. Then the Germanic races would have conquered the world.”
The Grand Mufti of Jerusalem Haj Amin al-Husseini energetically recruited Muslims for the SS (Schutzstaffel), the Nazi Party’s elite military command. He recruited Muslim volunteers for the German armed forces and was involved in the organization and recruitment of Muslims into several divisions of the Waffen SS and other units.