Saya route is new, i forgot about that. And yes as "rivals" the ninja eventually do die off as threats, that said they are the only faction that can attack your craft in flight, so they are still a problem well into the game, even if the ground combat gets easier. Also never underestimate a ninja's melee threat, they have the stats to really do a number on your gals when armed with fuso swords.
Buying
Oh, I forgot about buying people - I have about 1.5 billion and have been trying not to buy; I don't know, I just feel I have not tried, but when the only ninjas I have seen in the last actual 3 months have been about once then I think - it is a mechanic of the game to buy tech too.
Yeah buying VIP captives is the ingame solution to the highly streaky mission generation randomization. Factions can vanish for in game
years sometimes, so there is usually alternate routes, or the ability to just buy your way out of the problem. Like after a certain point you have funds to spare but are stuck on tech gates, might as well allow you to buy away the bad RNG so a campaign doesn't take needless extra time.