I guess I can't say this with certainty, but I don't think Seiga's encounter in WaHH 12 was part of the standard "every hundred years" thing that the Ministry normally does. First of all, it's always been said that Shinigami do that, and indeed people like Tenshi have actually fought shinigami every hundred years. Komachi herself says that shinigami never reap souls, and that those who do are something scarier (kishin). What this all implies to me, assuming there's no lying or retconning involved, is that shinigami normally fight hermits and celestials as a non-lethal test every hundred years, while when the Ministry really wants someone dead they send a kishin. And they really want Seiga dead.
This gibes with the fact that everyone and their mother seems to hate Seiga or at least recognize her as an evil abomination. The series is light-hearted enough to make a joke out of it, but she's literally evil. Heaven rejected her, she's called a wicked hermit, Byakuren's "Detect Evil" sensors are blaring wildly, etc. She disrupts the divine providence of samsara, uses unholy magic, etc etc. Seriously bad news. I really don't see why Heaven would suffer such a person to live if they can help it, much less "play fair" the way they do with the good hermits and only send an assassin every hundred years. And no hard feelings between attempts? Eh, samsara wasn't that important anyway.
Furthermore, she was apparently caught off-guard. You really think she wouldn't be counting the years between assassinations? I mean, she's confident but in the end she doesn't want to die. And Hell wants her to die. She's not paying the Ministry off with good deeds like Kasen is, so why exactly does Kasen need to that if they have the same standing?