I can't think of one good reason for leaving them in place. In addition to reasons you give for removing them,they will be in the way while doing work in attic like adding electric circuits,fire suppression and light fixtures. .

If the attic is unconditioned you want a good air seal at the ceiling below. Do whatever is easiest to air seal the ceiling plane.

We abandoned ours in place. We unscrewed the registers, set new sheetrock in the fill the holes, taped, floated, textured, and painted.

I'd definitely patch over the old ceiling registers but unless you plan on using the attic and need the space, or you're putting in new insulation, some things are best left undisturbed. Do you think you might have asbestos up there?

If you can get the ductwork out without a lot of work and mess, I'd do it. But, as others have described here, you can also weatherproof with the ductwork left there as long as it doesn't interfere with putting in sheetrock patches.