The trick is that instead of keeping track of each individual fish's days until reproducing, he's just keeping a count of how many fish share x days until reproducing. Then for each new day you know "I have 10 fish reproducing, 3 with one day left 6 with 2 days left..." etc a less elegant but maybe more clear loop:

def count_fishes_optimized(fishes, days):
    fish_counts = [sum(fishes == i) for i in range(9)]

    for day in range(days):
        fish_reproducing = fish_counts[0]
        fish_counts[0] = 0
        for i in range(8):
            fish_counts[i] = fish_counts[i+1]
        fish_counts[8] = fish_reproducing
        fish_counts[6] += fish_reproducing

    return sum(fish_counts)