It's not about Bowen and Horry making up for the big three, it's about the absolute freefall in toughness, clutchness, and intangibles from the Bowen and Horry replacements: Jefferson and Bonner.
Bowen could go scoreless in a game and still help the Spurs win with his incredible defense and effort. Jefferson goes scoreless and screws the team with his lack of all those other things.
Horry could miss threes but play incredible defense, grab huge rebounds, get sneaky steals leading to fast breaks, draw fouls, draw technicals, get huge blocks, and help the Spurs win in so many ways. Bonner misses threes and gets destroyed on defense, needs help on defense everytime making the defense suffer, get clobbered and thrown to the ground while trying to block out, pitter-patter about like a wayward chicken, and do nothing to help the Spurs win.