Are there 2 letter ISO codes for the pinyin or hepburn transliterations? If not, are there non-ISO abbreviations in common use? Thanks.
ISO has codes for languages (ISO 639), and for scripts (ISO 15924); but it has no codes for transliterations, as you can see by perusing ISO's standards on Writing and Transliteration. ISO adopts and standardises transliterations; but unlike languages and scripts, it has not catalogued them.
Using existing ISO codes, zh-Latn means "Chinese in Latin Script", and zh-CN-Latn means "Chinese in Latin Script, localised to China"; but that just implies "Pinyin" (and what country would we attribute Hepburn to?) It is not a solution.
I can't find evidence that there are standard codes for transliterations anywhere else either. A 2011 IETF RFC draft for transliteration codes went nowhere.
ISO has some standard romanization systems listed at https://en.wikipedia.org/wiki/List_of_ISO_romanizations. Pinyin is ISO 7098, but unfortunately no other systems of Chinese romanizations have been given ISO codes so you may not find this useful.