Separating character, equipment and animation is the right call, and the thing that usually breaks it later is not the art. It's the anchor.
A single offset per equipment slot holds up until the arm rotates. Once it does, the weapon slides off the hand on the frames that matter most. What fixes it is a small per frame anchor table, x, y and rotation, stored next to each animation, with the equipment layer reading that rather than a slot constant. It is boring data and it is the difference between a workflow that expands and one that quietly caps out at two weapon types.
The other one that catches people is draw order flipping mid animation. On a swing the weapon is behind the body during the wind up and in front on the follow through. If layer order is fixed per slot, half of every swing reads wrong. A per frame front or back flag beside the anchor solves it.
Last thing, and it's the reason separated layers sometimes read as stickers: pick one lamp direction for the whole pack and light every equipment piece from it. Mismatched light is what the eye notices before it notices the seam.