I'm using pandoc 1.9.2 with the bibliography command line option and a bibtex file. It contains some titles with species names written in italics (according to the nomenclature). I did this by surrounding them with the emph command. Unfortunately, this is ignored in the reference list of an HTML output. It seems hs-citeproc or some other part of pandoc ignores this latex command within bibtex titles.
I also tried the \textit command, without luck. I also tried other CSL files (nature, BMC Bioinformatics,etc.).
Since CSL 1.0 supports in-field markup like superscript, subscript, italics, boldface, etc., I assume it is not related to the CSL files. Instead, I assume it is related to hs-citeproc or pandoc.