Yes. that's great if you've got straight line access from above, but if the cell holder is between two PCBs, mounted on one of them, you'll need the magnet on the side of a tongue depressor or similar stick - at a pinch, stuck directly to a flat bladed screwdriver and taped into place.
N.B. if the shaft of the magnet tool is conductive and the magnet is plated or otherwise conductive, you should insulate the shaft or the magnet face with tape to avoid the risk of shorting the coin cell's +3V to nearby boards or parts.
The other advantage of a magnet over a suction tool is the coin cell will jump to it as soon as its loose if its close enough. Unless the suction tool is *VERY* high volume, if the cell tilts as it comes out of its holder beyond the ability of the rubber cup to accommodate, it is likely to break the suction.