That's odd. I have a script which goes through the XML files and figures out which ships counter each other. In the base game, the only structures my script finds which counter Fusion Bombers are DireGravityGuardPosts and FortifiedTestlaTurrets. By contrast, the Assault Frigates are vulnerable to Pike, Sabot, and Nucleophilic guard posts and turrets, which should be way more common in practice. Maybe the expansion added a bunch of stuff that counters bombers? Or more likely the bombers are just higher cap and thus individually squishier, or the durability ratio between strikecraft and frigates means the frigates hold up a lot better under heavy fire.
I definitely agree that Fusion Bombers should not require Force Field Frigates to be viable. I didn't particularly feel that fusion bombers were vulnerable in my last game, but they were never as highly upgraded as my primary units and I generally threw everything I had at big turret piles.
Your script is only looking at explicit damage bonuses and not any of the other things that make up unit counters, like DPS/HP ratios, refire time, multishot, wing size, etc. For example, Assault Frigates perform much better against multishot, beam, and AoE turrets than Fusion Bombers and don't get overwhelmed by swarms because they have a multishot weapon with a short refire time. You are correct that the DLC adds more turrets that counter Fusion Bombers that also wouldn't be flagged by your script; for example, the Holocene turret is an infinite range high-burst-damage AoE turret that performs extremely well against slow strikecraft, but does not have explicit damage bonuses against any unit statistic.
Additionally, a bunch of small units will always be worse than the same total amount of HP and DPS in a single unit, because the only hit point that matters is the last one. The small unit swarm will lose DPS as it takes damage and members die, while the large single unit loses no DPS until it loses that only hit point that matters. MK1 Fusion Bombers have 4800 HP, 2400 shields, and a 30 DPS single target weapon with a 6 second refire time. MK1 Assault Frigates have 165000 HP, 83000 shields, a 700 DPS single target weapon with a 3 second refire time and a 1067 DPS 8x multishot weapon with a 3 second refire time. The starting wing of 40 Fusion Bombers has a total of 288000 HP+Shields and 1200 DPS, split across 40 units. A theoretical starting wing of 2 Assault Frigates would have 496000 HP+Shields and 3534 DPS, split across 2 units. Wings you get from ARSs have an average of 32 Fusion bombers or 1 Assault frigate, so 230400 HP+Shields and 960 DPS split across 32 units for the Fusion Bombers and 248000 HP+Shields and 1765 DPS for the single Assault Frigate. Assault Frigates not only benefit from being a single unit and thus not being vulnerable to AoE/Multishot or losing DPS from taking damage until losing the last hit point, they also just have more total health and DPS.
Fusion Bombers have greater frontloaded single-target damage, as they fire once every 6 seconds compared to the Assault Frigate's 3 second refire. They also have much higher shield penetration, 100% for the Fusion Bombers compared to 60% for the Assault Frigate's Fusion Bomb. The Assault Frigate also performs worse against single targets, as its 1067 DPS Point Defense weapon is Multishot and doesn't have any shield penetration at all. So in the situation where all of the Fusion Bombers survive the approach, they perform better than the Assault Frigate against single targets, at least until they start losing wing members. This requires a Forcefield Frigate and unit micro to keep the Fusion Bombers underneath the Forcefield Frigate. Assault Frigates do not require the same level of protection or micro and perform better after taking damage; they will be better than Fusion Bombers if the Forcefield Frigate is removed, as well as better for new players just smashing their fleet into an AI planet without microing anything.