I noticed while looking over Biohacker that it's got some similarities to Operative. 3/4 BAB class with built-in debuffing.
I'm going to make the following assumption in my comparison: you can ignore theorems and exploits in the comparison. They're both traded by archetypes, and if any particular exploit or theorem is needed to make the chassis competitive, it's too much of a tax. I'm also only looking at Int-based Biohacker, as it's the most comparable. I'm still bringing a hefty amount of bias to the table, so get your grains of salt ready.
Operative: 10-12 skills, Dex primary, +1 to skills, trick attack (~55% for +1d4, +2 attack), two good saves (one of which is beastly)
Damage: 1d4 + 55% of 1d4
Biohacker: 10 skills, Int primary, +4 to Perception/Sense Motive, +1 to attack, basically two good saves (and starts with effective +2 will), 5/day debuff for two rounds of -2 AC or a couple other options, or +2 to skills for a couple rounds. Plus, a cool scanner.
Wow! That's WAY closer than I thought! The ability to use Int for will saves and the two Wis skills means you can be as skill-focused as a Dex-focused Operative. You've got a more reliable attack bonus, but you're stuck with worse weapons. You're more party-friendly, but stuff like your skill bonus is very limited in time. Your combat abilities are limited use, but trick attack has a limited chance of success.
Operative: Now doing serious damage, gets a fancy ability. Now provides 1-round debuffs on the level of what Biohacker's defaults are. Also, evasion, bonus move speed, and another +1 to all skills.
Damage: 1d8 + 2 + 55% of 3d8
Biohacker: Biohacker gets a 1/day super-debuff, and no longer has to worry so much about running out. Breakthroughs are mostly circumstantial, but the free use is good. If you want to load up the party, though, you're going to be spending down the durations of other ones pretty hard. Is it a problem for them to last long enough to generally assume they're up? Probably so, they'd need to knock down some of those bonuses hard.
Damage: 1d6 + 2
Biohacker is getting a little nervous now. Operative gets in on helping the party in combat, and Trick Attack is dishing out a lot of damage when it's successful. Biohacker has more uses of their injections, though, while Operative still has ~55-60% chance of succeeding at trick attack. Biohacker also has a possibly useful breakthrough at-will, and a 1/day ability.
How much better is Biohacker at debuffing? Sickened vs. off-target is probably a good example. -2 to hit is probably about the same as -2 to saves, and skills/damage aren't as big a deal. So, the debuff is about twice as good, and lasts longer (but takes resources to renew). Operative is about twice as good at damage, from the looks of things, so we're still okay.
Operative: Trick Attack is stronger, now effectively guaranteed. More movement, better skills. Is triple attack good? I don't know the math.
Damage: 2d6 + 5 + 5d8
Biohacker: Biohacker is now 2/day on the double debuff, gets a very, very small improvement to the scanner, gets another set of injections, and gains +1 attack.
Damage: 2d6 + 5
Here's where it seems like Biohacker really starts falling behind. Operative is more than twice as good at damage, and Biohacker is still only twice as good at debuffing. The duration doesn't matter much anymore, with Operative refreshing every hit.
Almost everything an Operative gets scales in power. Biohacker scales in options and uses, but a given round doesn't get more powerful outside of the accuracy bonus. That accuracy difference disappears when you give Operative an energy weapon (reflected in the damage), and with Trick Attack resolving against flat-footed AC.
Biohacker has more options, and nearly as many skills, so they probably shouldn't be doing as much damage as the Operative. But… as of level 7, Operative is doing way more damage, on top of being more mobile and doing about half as well at debuffing enemies. Biohacker's breakthroughs can be considered comparable to the 5th and 11th level unlocks of Operative. It feels to me like Biohacker needs to spend theorems just to avoid falling too far behind Oparative's chassis.
If you take the theorem at level 9 bio hackers can at least do full level as bonus damage with injection weapons. Also weirdly enough if a biohacker is really trying to optimize for damage it looks more and more as I look at the item lists if melee is not the way to go.
Ice Needle, Artifice Cryo 10 18,400 4d6 C & p injection DC +2 L conceal, injection, powered (capacity 40; usage 4)
So if you are a melee speced biohacker you would be doing 4d6 +10+whatever your str is damage. They also would be +2 to hit on it without even going into any feats they may have taken for weapon focus.