Blizzard has made this impossible with the launch of Mists of Pandaria. When they introduced vignettes, the old cache system went away and none of the previously-existing rares were updated to use that system.
What I've done, personally, is turn on nameplates and set them to always show. Another option is to use a targeting keybinding, which you'll find under the WoW client's keybinding menu. Unfortunately, that entails constant key-mashing.
Which NPCs is this happening with? If they're older NPCs which aren't tied to an achievement or have no tracking quest, the only thing you can do is manually ignore them. If they aren't either of these, that means they're missing attribution.
When the targeting frame appears, you can hover over the X button on it and you should see the option to ignore via right-click.
Not only can I not reproduce this, but I can't fathom how this would even be possible since NPCScan doesn't touch trade skills at all. Please install BugSack and try again - you should get a Lua error when you cannot open your profession window, which will tell you what and where the error occurs.
The new range is intentional, and is more in-line with the behavior pre-MoP when deleting the cache was a thing. When Blizzard took this away, everyone lost their minds because they were restricted to nameplate and minimap range. Now that BfA has changed things yet again to allow for longer-range detections, that is being complained about. There's no winning!
No, Blizzard made a stealth change in the latest mini-patch that affects ChatLog stuff which LibSink handles. I'll push an update to address that soon, but if you've already updated other AddOns that use LibSink it should fix them all due to the nature of how libraries are typically handled.
That was actually the plan, but I want to have a centralized point that affects both the list addition and the tooltip display, as well as a place to turn those off the preferences. I haven't had the time yet, though, since I'm currently on vacation visiting family and need to rewrite _NPCScan.Overlay and Archy - those are taking precedence.
Overlay needs a complete rewrite. Not only due to the binary encoding issues with CurseForge, but with WoW 8.0 Blizzard has completely replaced the map system. I have no ETA right now, since I have several other projects that require my attention. At the moment, I'm in the process of rewriting Archy for the same reason.