Is Sakya short for Shakyamuni clan?
Sakya refers to the place name of the main monastery of the Khon family lineage in Tibet. Sakya means "grey earth". Other transliterations are also possible: Sa skya, I think in Hopkin's system he transliterates this to Sa ga.
Shakyamuni indeed means Sage (muni) of the Shakya clan. The Shakya clan was a clanal/tribal unit in north India. They were basically wiped out in a war during Shakyamuni Buddha's lifetime.
You are confusing coincidental transliterations from Tibetan and Sanskrit that just happen to have several phonemes in common.
Shakya != Sakya
_________________Kirt's Tibetan Translation Notes
"Only you can make your mind beautiful."
HH Chetsang Rinpoche