Yeah, every engine I've ever worked on has a harmonic balancer. Its attached to the crank and should dampen vibration caused by firing of the cylinders. I assume tractors would have them as well, but never took one apart to see. In older engines, the fly wheel generally has a lot of weight to help dampen the bursts of power from cylinders firing.
My opinion on the 4-cyl vs. 3-cyl debate- More is better, but will probably take more fuel to run. Cars often have same horsepower between high-end 4-cyl and mid-range 6-cyl, or high-end 6-cyl and mid-range 8-cyl engines. Even though horsepower is the same, it seems like more cylinders makes more power. Not sure why though.
Usually, if the pistons are smaller, the engine turns higher RPM's. So for a 4-cyl tractor, its probably going to run 3200 rpm for 540 PTO rpms, which is where the power band is. With 3-cyl, its probably more like 2700 rpms for 540 PTO rpms. And keeping the engine in the power band under load is the trick.
The higher rpms usually feels like you have more power. I don't know if you actually have more power, because in theory it should be the same. But I know that more cylinders and higher RPM's "feels" like more power in most cases. The trade-off is that at 1000 rpms or less, it feels like more cylinders has less power. So at low speeds, torque will be higher with bigger cylinders turning slower. And often people run tractors at low rpms, so I think that is why 3-cyl is more popular than 4-cyl. That's my unscientific opinion, but if you take some test drives, you can probably feel the difference yourself.
What you should do is analyze your intended usage. If you plan to run attachments all the time at high rpm's, get the 4-cyl. If you plan to use your tractor like a utility tool doing anything and everything, get the 3-cyl.