-- Last Updated: Jan-05-13 8:48 PM EST --
Check the rating on the existing cylinders - it's often printed right on them, or you can measure it with a bathroom scale. If Thule says the device is rated to lift 40 pounds, you can be sure that the force applied by the cylinders is greater than that, most likely MUCH greater. That's because, due to their placement relative to pivot points and load location, the cylinders are working at a mechanical "disadvantage".
You can see this same principle on the lifting cylinders for the back window of a pickup topper. On my current work pickup, a pair of 20-pound cylinders won't even hold the window up. A pair of 40-pounders is overkill, but it's what I could get my hands on. The whole window probably only weighs 18 pounds, so just ONE 20-pound cylinder could hold the window open if the force were not exerted in such a disadvantageous manner (the force that must be applied fairly close to the hinge point is huge in comparison to the weight of the window that is actually lifted).
The same principle applies to your Thule Hullivator, but the difference between lift capacity and lifting force that must be applied by the cylinders will depend on the geometry of the device. **Edit** Okay, I just looked at pictures of the thing online, and sure enough, the degree of mechanical disadvantage is huge. Therefore, the force generated by both cylinders together is going to be much greater than the 40-pound force that is actually applied toward lifting your boat. That doesn't mean you might not be able to find cylinders that can lift more than the factory originals. It just means the rating of the cylinders you seek will be a lot greater than what you are thinking. On the other hand, I don't know if the machine is robust enough to handle this extra force. How heavy a boat are you lifting? Once 40 pounds of that weight is taken off your hands, there's not much left. I load a 31-pound canoe overhead and there's nothing to it (all my other boats require special technique to make roof-top loading easy, but the 31-pounder can be loaded "the hard way" and it's still almost effortless). I can't imagine your share of the load will be much worse than that, and what's more, it's being guided and controlled for you too. I'm thinking the factory-original lift capacity should be fine.
One final thought: You say that installing stronger lift cylinders may reduce the problem of "unequal lifting", but I suspect that the opposite will be the case. Think about it this way, if you lifted the whole load yourself, you would make sure one rack didn't rise a whole lot faster than the other. This unequal-lifting problem is caused by the fact that when one rack gets a little "ahead" of the other, the geometry of the device causes mechanical advantage to increase (it's still a mechanical DISadvantage, but now, to a lesser degree). Use cylinders that can't quite lift their share of the load and this problem is easy to control because only YOU can provide that little bit of extra effort to raise the boat. Use cylinders that can easily lift more than what you ask them too, and whichever rack gets just a bit ahead of the other is really going to "take off", and the stronger the cylinders, the greater the magnification of this situation.