I suspect that some of this is down to context. (Also, some are talking about coming back after a long hiatus, and for sure, NPCs got 'better' with 2.1.)
In my experience, and I'm most definitely no top gun fighter ace, if you are in a 1v1 with an NPC, they are generally far from unbeatable. That obviously depends on their rank and ship.
However, if you get into a situation where you are taking on multiple NPCs, then that is a different thing. NPCs shoot at you now, and they hit you. Prior to 2.1 I could happily take on a wing of 7 NPCs, and they lined up dutifully to let me shoot them, that no longer happens, and any NPCs in a wing will all go at you at once, and if you are being shot at by two or three lots of weapons at once, then your shields take a battering.
As to them having engineered weapons, I am pretty sure they don't. Perhaps the odd Elite one will, but in the main, they simply now pack better, more powerful weapons like PA's and rails, and they are able to hit you with them.
I do have modded shields on most of the ships I expect to do combat in, but only up to maximum grade 3, so not overly strong, and I find that they tend to hold up fairly well 1v1, but if I find myself outnumbered, then I generally get out.