Youki's name consists of two kanji: You (妖) as in "youkai", and Ki (忌) which mean "inauspicious" or "taboo".
The characters for Konpaku mean simply "Soul."
Although both "Kon" (魂) and "Paku" (魄) are "soul", their elements are different. "Kon" stands for a mental soul, which is separated from a body as soon as human dies and ascends to Heaven; "Paku" is a physical soul, which remains in the body a few days and goes back to the Earth. In this case, "Kon" is Youki's phantom half, and "Paku" is human half. Maybe "Konpaku" is not only be a surname but a feature of his race.
Youki is one of a few male characters in the entire Touhou series, as most are all female.