You need at least 50 fighter squadrons to counter effectively and quickly. About 30 will reduce the 100 bombers but wont knock them out until their carriers run out of antimatter, which takes a long time.
That assumes no enemy flak eating your fighters...
Early bomber spam can be dealt with via corvettes + disciples...if coupled with titan, that's a little more difficult, you'll have to go with fighters, flak, and/or corvettes (flak and corvettes would be microed to avoid titan AoEs)....
Late game though, the only thing that's really effective is multiple caps with anti-SC abilties...that's multiple Kols, Halcyons, or Kortuls...fighters/flak combined with multiple anti-SC caps will work pretty well, though you may lose some caps depending on what faction you are and the stats of your caps (number/levels)....