Where is it stated that Species 8472 are experts in genetic manipulation?
Species 8472s ships were bio-tech, indicating that they have a fairly advanced form of technology in that area. Plus their ships could not be assimilated either, which hindered the Borg as well.
If the Founders engineered the Vorta to be immune to all forms of toxins, surely they can engineer them to eradicate all foreign substances (which is toxins, correct?) if they aren't already immune, rendering Borg nanoprobes useless. In a head on conflict, which is what this thread is asking the borg lose... Why?
The Vorta are immune to
most forms of toxins, not all. Still that's different from having tiny little robots injected directly into your blood stream.
What they can't assimilate they can't understand, adapt to, or analyze.
The Borg don't need to assimilate individuals to learn what they need to know. They can still assimilate the Dominion's technology from capturing ships, stations, planets, anywhere where there is a computer system they can interface with. All it needs is a Borg cube to run across a Jem'Hadar attack ship, catch it in a tractor beam and blow up its life support or cut the hull open...then the Jem'Hadar are dead and they have a nice little ship to have a look at. Plus there is the old fashion, let's study the corpse method.
Assuming that the Founders could make the Jem'Hadar and Vorta immune to assimilation, which I think is an extremely tough ask, that doesn't mean they would win.
They can also the Federation, Klingon, Romulans or Cardassians and assimilate the knowledge on Dominion tactics through them. If they are really in the need to understand the Dominion that is.
Plus I remember Damar had a plan to poison the KW to kill the Jem'Hadar. So they they suggests they could be poisoned as Damar's plan was to kill the Jem'Hadar instantly before they went crazy from lack of white. The Jem'Hadar didn't take too lightly to that suggestion either, so maybe it was possible or perhaps they were just pissed that their ally was thinking of ways to kill them.
Though Weyoun didn't seem to concerned about the plan. Either he already knew of and approved of the plan or maybe he thought it wouldn't work for whatever reason.
2. Jem'Hadar are genetically engineered. They can be modified to be immune to assimilation, but I'm quite sure that they are already. Why would the Founders create a species that can get "sick (meaning invaded by foreign bodies because thats what sickness is)?" They don't sleep, they don't regenerate, they don't eat... so why would they be in danger of assimilation?
On the chance they could not assimilate the Jem'Hadar or Vorta, then they can just kill them. Wage a standard war, transwarp in and destroy KW plants, breeding centres, shipyards. The Dominion also have no way to strike back and damage the Borg's industrial might.
3. Changeling infiltration.... forgot about that? Changeling poses as a drone and does what it has to do.
The Borg are a hive mind, a Changeling could not just walk in and say, "Hi, I'm 23 or 28. I'm a Borg, what are your weaknesses?" The Borg would find it strange that they weren't part of the collective. Plus despite this ability it they still lost the Dominion War.
The Feds used blood screening and phaser sweeps to detect Changelings...Borg could do the same or have funky Borg methods. I wonder if their eye device that could disrupt holograms could do the same to a Changeling?
4. The Collective is one mind. A single virus will affect the entire species. Remember that GENETICALLY ENGINEERED Teplan Blight that was modified to ONLY affect the Teplans? Yeah, they are mediocre at genetic engineering...
And it took Bashir all of 2 weeks to make the next generation immune to the disease.
Though I do think a magic anti-Borg virus is the only way the Dominion could beat the Borg. The question as was brought up above is would any theorised virus work in practice? We don't know.
5. Uh... Jem'Hadar shroud. All of them.
Borg have better sensors, they might be able to detect Jem'Hadar even when shrouded. Once they do unshroud they would be open to attack as any other species.
6. Jem'Hadar don't have to use phasers like the other weak humaniods. They have swords and are several times stronger than humans.
Stronger then humans doesn't seem to mean much in Star Trek...I seen Sisko
beat several Jem'Hadar and Klingons in hand to hand combat. Plus for the most part we've seen that the Jem'Hadar use energy weapons more then bladed weapons in combat.
Klingons are stronger then Humans and so are Vulcans but the Borg seem to have no problem with assimilating members of those species.
7. Jem'Hadar are grown in hatcheries, Borg need to assimilate to grow, otherwise their stuck in maturation champers. Jem'Hadar take 3 days to mature, Borg drones take about 25 days(reference: "Drone").
They can breed Jem'Hadar quickly. The Borg would then target these facilities and try to destroy them to disrupt their supply, plus attack KW plants. On the other hand, the Dominion can only strike at Borg planets and ships in their immediate area. The Borg's vast Delta quadrant empire would be untouched.
Plus it takes minutes/hours to assimilate a fully grown humanoid. The Borg can top up on drones at the Wadi homeworld, or Karemma, or Dosi. Plenty of races out there to supply the grunts.
8. The Dominion build ships faster than any known species.
We have no idea how fast the Borg can build ships. So we don't know how they compare. Borg can once again attack shipyards and disrupt the supply of warships, Dominion cannot do the same to the Borg.
Prepare for ramming speed.
Ramming is a great tactic against the Feds and those people because it carries an extra psychological factor, one that would be lost on the Borg. Then it comes down to how many ships it takes to destroy a cube by ramming and whether or not the Dominion can withstand losses it would incur in the ramming and the number of ships lost to Borg weapons before they get close enough to ram.
Given transwarp, Borg ships could also outrun Dominion fleets, making it easier to avoid engagements when necessary.