They do seem to be one of those things that could be "toned right the hell down". I know it's meant to be a game with some challenges in it, but it's also meant to be fun to play. That the ninjas group-up repeatedly in early-mid game doesn't allow for all the fun-bullshit to happen, or even expansion of options on how you want to play, or options for it, which is essentially the point of an xcom/any-mod playthrough, which removes the joy of this. Try and play it how you want, even with certain challenges, even a bit slowly, but not too slow. Discover and be immersed in new content and factions and lore and challenges contained in the mod. But there's not meant to be "must do this, or fail". It's meant to be fun, a certain amount of power-fantasy, and still have many challenges. Some of which you're not prepared for, some of which you are, but not walls there-of. It's not meant to be a waste of your time due to mod-mechanics that crop-up regularly in many people's games that shut entire playthroughs down.
This is not a roguelike. It's not meant to be a save-scum either.
Ninjas seem to not fit properly into many people's playthroughs, so should be altered and toned down. Or scaled sufficiently that they're not an unenjoyment wall. Or removed until the time that they can be at this level of additional enjoyment to playthroughs, instead of the negative they still seem to be (similar to slightly overly high armour and sight and reaction values on some mission-turrets. They're meant to be tough, but they're meant to be blown-up, by the player, even without truly optimal play or game-engine knowledge. A cool feature, a set-piece, not a "don't go there bitch, unless you've got this-much-shit!" so early on in the game). Make them tough, but make them enjoyable to kill.
(I've never thought of xpiratez as some weird DDR or Cataclysm-DDA roguelike-experience, where certain things are assumed for the gamer to have-to-have-to-do, or the developers jumped off a cliff gameplay-wise to provide you a cliff-like learning-curve experience on the game/mod they were developing. It's usually been fun playing it. It seems like the ninja-base-bullshit is detracting and detrimental to the mod, so should be fucked right off until it feels fun and enjoyable and balanced. So says I)
((And yes, this is on a Dwarf Fortress forum. Because, there's something to be said about "not making games/mods as messed up as DF is, learning-wise", for players of said game/mod. I mean, it works, really really well))