There are a number of factors. Longevity, health, bonds used PEDs, and it was before the era of analytics and pitching science. It’s harder to hit than ever. Teams use their bullpens aggressively now whereas starting pitchers used to pitch 7 or 8 innings routinely in Bonds era. Teams take guys out in the 4th and 5th inning now unless they are elite pitchers or dominating or trying to eat up innings so they can optimize matchups with their bullpen. It is a lot easier to hit when you see the same pitcher 4 times vs 3 different pitchers in a game. Also, teams have invested a ton in trying to maximize pitching. The Blue Jays have a pitching lab in Florida where they send their guys to get analyzed. Everything from their windup, release, follow through, the shape of their pitches, spin rate and so on. They will take all this data to improve guys, determine what pitches to throw in what location and what situations but also to match with opposing hitter data to determine the best matchups and ways to pitch to guys.

Long winded answer but it’s harder for Judge to hit off 3 fresh guys who have a team of physicists telling them how to get you out than it was for Bonds to hit off a guy who throws 3 pitches you have probably seen a hundred times. Not taking anything away from Bonds, he was the best hitter of all time.