You don't need more surface area to have more holes. You just need a stronger material that will allow more holes without deforming.
Let's try this again...
Let's say you have a surface area of 10 square inches. In order to get more holes into the same surface area, no matter what the medium is, you have to make smaller holes. There is a finite number of holes that can be made in that surface area, just as the minimum number of holes is one.
Obviously one big hole is not going to restrict air flow. As you add holes, they necessarily have to be be smaller, which will restrict airflow relative to one big hole. Now, as you point out, you run into a problem with the medium being strong enough to hold together but let's (for the sake of argument) assume that the medium will NEVER break no matter how many holes you put into it. Eventually, and this is where physics comes into the deal, you will reach a point where they filter reduces air flow simply because of the size of the holes will not allow the gas molecules to pass through except in single file.
Now, in the real world, you get to that point long before the number of holes weaken the medium to the failure point. The reason that OEM filters restrict more than aftermarket (like K&N) filters is because the holes are much smaller, not because there are too few of them. If they tried to add more holes, they would have to be smaller than the holes in the OEM filters (especially Toyota filters, as they use fiber filters rather than the paper kind with holes in the 120-130 um range) which would further restrict airflow, but for a very practical reason... the very contaminants that the filter is trying to keep out would clog those smaller holes very quickly. So there is a practical limit to how small the holes can be before you literally starve the engine of air.
The other way to add more holes is to increase the surface area, which is why most filters are folded into pleats. More pleats gives you more surface area but even that has a practical limit as you can only fold things so many time before you effectively turn it into a brick.
Keep in mind, every bit of technology in an IC engine is 100 years old. Engineers have refined it, found better way to control it, and made it more efficient but they haven't fundamentally changed it because there are practical limits to what can and can't be accomplished using that technology. Air filters have been pored over by engineers for decades in the search for that perfect balance and aside from advances in filter media, we've hit the wall as far as air filtration goes.
