I like needlework and do a lot of long-haul, so I feel for you.

How big are the "large needles"? A bit bigger than standard sewing needles, or nearly knitting-needle size?

Can you use plastic (or other non-metallic) needles? They might not be so prominent on the x-ray or appear as dangerous if they are noticed.

I sometimes travel with a little zippered bag for my laptop cord, phone charger and other wiry techno things. If by coincidence a needlecase was tucked in with all those other long thin metal bits, it might not draw attention.

You seem to have solved the scissor/nail clipper problem with the dental floss container, but another option is this: Clover thread cutter

My concern about sewing on planes is not just getting through security, it's some anything-for-safety paranoid idiot in the row behind seeing me doing cross-stitch with a 2.5" needle and reporting me to the flight crew.