Composite kayaks are made, on the whole, in 2 parts. They will be made in a 2 piece mold, the mold is bolted together, and then reinforcement is added around the inside seam that forms.
To add additional strength, an external seam can be added around the outside.
If you wanted to make the seam invisible, then they normally spend time polishing the seam out so that it is very difficult to see a join. But this takes a lot of time and effort.
To make it in a single piece is possible, but would take a lot of time and trial and error to do. You would need to lay the boat up with the mold halves together and get the fabric into all the corners with no bridging, this is not easy.
In terms of the "painting" you mentioned, there are 2 ways which kayaks are being done at the moment. The most common method being that it is a pigmented gelcoat they is put int eh mold first to give the design. A lot of newer boats have gone down the route of being sprayed post production with a 2 part polyurethane, something I would not recommend as it requires a lot of safety equipment.
Aligning the halves together after making is a simple job, if he mold is made well, it will take no more than 10 minutes. The strength if the finished part is just as good for a kayak as a single piece would be.
I have made a fair few kayaks in the last few years and are all still standing in one piece!
Anything else let me know,
Tom