Yes there were Muslims in the Balkans in WWII. In what is now Bosnia-Herzegovina they fought on both sides of the war, some for the Yugoslav Partisans and some for the axis-allied Independent State of Croatia (NDH). There was even a Muslim SS unit that fought for the latter. Treatment of Muslims overall differed by ethnic group and political leaning - some embraced them, some were indifferent, some were outright hostile. I can source this when I get to a computer.

I'm not too familiar with the other areas with significant Muslim populations (Albania and Bulgaria) at the time.

As far as hijabs go, many women (especially older women in rural areas) wore (and still wear) similar headwear so hijabs wouldn't really stick out as much as they would elsewhere in Europe.