I am aware that the Kedusha is in hebrew, of course. The first two words, though, in some nuschaot are in Aramaic, I believe. ... Again, I am no diqduq expert but if those words were in Hebrew and in the feminine form as you suggest, they would have read Naqdishech v'na'aritzech - both with a tzere.
Sephardim many times say female words in Hebrew in reference to God, throughout the Siddur.
No need to analyze it.
You're absolutely right that there is no need to analyze it, but it's not actually feminine. Dikduk has evolved over the centuries, and during Mishnaic times this was the Hebrew masculine form. It is used throughout the Sefardi siddur as it was, rather than changed to suit contemporary usage, as in the Ashkenazi suddur. See the writings of HaRav Matzliah Mazuz, and his son the Rosh Yeshiva R' Meir Mazuz for a real explanation. He goes into far more detail on the dikduk of the siddur than I think you want here.