Loving the answers to this one almost as much as the idea of throwing a magic boat at people. Gotta love inventive players, even when they mess up your carefully laid campaign.
Scott's treatment of the physics of the problem is great, but might be missing the application of magic to the issue.
The description of Catapult I found reads (in part):
Casting Time: 1 action
Range: 150 feet
Choose one object weighing 1 to 5 pounds within range that isn't being worn or carried. The object flies in a straight line up to 90 feet in a direction you choose before falling to the ground, stopping early if it impacts against a solid surface.
This indicates that the spell is moving the object but not imparting momentum to it. Which makes sense since, as an instantaneous spell the momentum would be infinite anyway. In a science framework this would be immediately objectionable, but we're using magic so I have no issue with it. It's just a teleport spell with some odd side effects.
The remainder of the description talks about the damage done -
(cast level + 2)d8 - and the maximum mass if the object -
cast level * 5 pounds. The actual mass of the moved object doesn't factor into the calculations of the damage or how far the spell can move the item, these are set as parameters of the spell itself. This is why there's no difference between using Catapult on a 1lb bag of feathers or a big old ball of sharpened spikes.
So what happens if you cast Catapult on a Folding Boat and invoke it in transit?
According to the spell description above you actually can't do this. The duration of the spell is instantaneous and as such you can't perform any other action during it. The Folding Boat would disappear from one place and immediately appear in another, unfolding either before or after the move.
So even if you time your activation as close as possible to the release of the spell, the unfolding will either happen before or after the spell effect takes place. If before then your folded boat is transported and strikes the enemy, both taking 3d8 damage from the spell, then unfolds. If before then the boat takes on mass that makes it an invalid target for the spell and thus the spell fails, causing no damage to either boat or target.
Let's assume that the unfolding of the boat takes time and is starting to happen when the Catapult spell affects it. Nothing changes except for the location of the boat as it unfolds.
So... +5 points to the players for style and imagination, -10 points for feasibility.
I can still think of a few ways that could be useful, such as knocking somebody down with the folded boat and then trapping them under it as it unfolds, or firing the boat into an enclosed space and having it crush the contents against the walls as it unfolds, but I'm pretty sure any GM I know would rule at least one of those out of practical use.