Well, the emperor filters have bio-wheels, so, you would mostly be losing out on mechanical filtration ... with that respect, yes, you can just remove the carbon. If you replace them as regularly as they require, they have no beneficial bacteria in them anyway (or not enough that matters).
Carbon isn't necessary anyway, but, mechanical filtration is. You can cut the top and empty the carbon out ... not easy to get it all though from my experience. You can also get some filter padding and cut it up to place it in those gray containers that came with the emperor for added mechanical filtration.
I don't use carbon, except for removing (chemical) medication, which I haven't needed to use. Carbon masks problems, and anything it claims to do, is taken care of by a water change. Saves a lot of money, since for carbon to even be effective, you need to replace it just about every week. A concentrated water treatment used with a weekly water change is much cheaper, and much better for the fish.
On to treating Ich ... you can use chemical medications ... but, I prefer the natural treatments, when possible, or when the problem isn't severe.
First, verify it is Ich. Does it look like salt crystal dots? I have known people that have mistaken a fungus for Ich because they weren't familiar ... not claiming you have done this, but it is always best to be certain to cure the right disease
I also ask this, because it is rare for one fish to be affected and not both with Ich by the nature of the parasite, but fungal and bacteria infections can more easily attack a fish first with a weaker immune system (though, so can Ich).
Ich can be treated by using heat and salt. If you have no other fish in the tank than the Oscars, you can buy freshwater aquarium salt and dose 1 tbsp per 5 gallons. When changing water, only replace salt for water you physically remove and not the evaporation as well ... or it can add up to more than 1 tbsp per 5 gallons quickly.
The heat part requires slowly raising the temperature in the tank 1-2 degrees at most every 6 hours until you reach around 88 degrees.
Now let me explain how the cure works. Ich is sensitive to salt. It kills it ... but, only in the free swimming stage. In fact, even medication can only kill Ich in the free swimming stage. Ich lives in three stages, attached to the fish, dormant on the gravel, and free-swimming trying to find a host.
The heat speeds up the life cycle. I have read reports from scientific organizations claiming at temperatures in the low 70s and below, the life cycle can be a month or more! But, at high 80s, the life cycle is sped up into a matter of days.
You are going to want to treat the whole tank, since Ich itself is microscopic, and any fish in the tank most likely has it, just not a large enough colony to see. The raised heat will also speed up the immune system of the fish and help them fight it, but again, any other fish you have in the tank, if any, you will need to check their sensitivity.
Continue this treatment for
at least a week after your temperature has been raised and salt added. This should be close to two life cycles of the Ich and prevent future outbreaks.
During the course of the week, do regular water changes and clean the filter boxes out to get any of the detached Ich, making sure to gravel vac well.
You can also use MelaFix and PimaFix in conjunction to aid the immune system against any other infection that may try to rear its head ... since the fish are already fighting one thing off.
After 7+ days of treatment, you can start slowly lowering the temperature in the same rate as you raised it, and stop adding salt to water changes.
Another note, an air stone to help with gas transfers is also a good idea, because as temperature rises, oxygen content decreases. Surface disturbance (breaking surface tension) is what helps with the water releasing CO2 and O2 getting back in
I know the emp 400s create a decent amount as well. If you don't have access to an air stone, leaving the water level down a bit so the water coming out of the filters 'splashes' more will also do a similar job.
I have never used the medication, so I cannot comment on it at all.
I will almost guarantee that your fish had Ich from the store, and it just took this long for it to multiply enough to be seen, that is, if it is Ich for certain.
If you have been using the medication with the carbon in, the carbon has been absorbing the medication and the treatment really hasn't started much yet.
I try to give cheaper and more natural alternatives when they are available.
Hope the best for your Os, and if you get some pictures up if you can, we may be able to verify Ich.
