htseq-count counts each read pair for the gene it maps to as long as it maps unambiguously to one gene. If one of the two mates could not be aligned, htseq-count uses the information from the aligned mate only.
What to you mean by "including single reads"? Do you have a sample with a mixture of paired-end and single-end reads?
What to you mean by "including single reads"? Do you have a sample with a mixture of paired-end and single-end reads?
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