It used to matter, because aircraft would sometimes approach the carrier at a lower altitude than even the flight deck before pulling up briefly and practically stalling onto the deck, allowing for a lower speed landing. Similarly, the higher flight deck would give an extra couple of metres of acceleration if over-shooting the flight deck and having to go around. As such a high-decked carrier gave a little more margin for error.
It makes virtually no difference - modern aircraft approach at the same angle and airspeed regardless of the height of the deck (within reason). They also perform approaches significantly more accurately. If anything, the higher deck could be considered a (very) slight disadvantage, as it may display a higher rolling moment than a low deck carrier. This is unlikely to cause any issues, however.