Does zygosity have meaning for mitochondrial variants?
You abosolutely can have mixed populations of mitochondria in a cell (it is in fact very common). Therefore when you sequence the mtDNA you will get a completely variable percentace of reads containing a variant from close to 0% to 100% (there is a lower limit based on the quality and read depth of the sequencing data).

You can't consider the variants to be heterozygous or homozygous as conventional zygosity doesnt apply. Heteroplasmic and homoplasmic are the terms which are used.