well, ninja buffed or not. it's the way of the world at cryptic. they keep pushing the bar as to how much damage we can do and then react with increasing the damage and hitpoints of the pve enemies. that's their way of balancing the scales.
yeah. at cryptic instead of making stuff smarter, they just give them insane powers. HSE is the best example. they wanted something hard, they just put a dozen oneshot ships there. it did not become hard, just annoying. a group of good players will be just annoyed, by the oneshots, but will finish it easily (I had 6 30k+ hits in one run, and I was not the only one, and we finished every optional easily, we were just annoyed, because there is not much you can do against those shots, if your shields are down)
still as long as shields do defend against these shots, there is no problem, and the only real issue remain to be the gates invisible oneshot torps, which can be avoided