A number of high end cable manufacturers can do custom configurations like splitters and Y's. Obviously, you're going to have to pay up and wait.
Your option #2, using a Y cable, may offer a purer signal path by eliminating one interface/connection (between the splitter and the IC's) that would exist with option #1. Theoretically, such interface/connection points could slightly degrade the sound. HOwever, I have used option #1 splitters with no observable difference in the sound.
Practically speaking, option #1 gives you significantly more flexibility if you ever want to change things around in your system. For example, if you went with option #2, you would have to get a Y cable with one leg perhaps 1 meter long to connect your preamp to your basic amp and the other leg would be perhaps 4 meters long between your preamp and your subwoofer, to provide for optimal placement of your subwoofer. This could limit your options if you ever changed your mind about subwoofer placement.
Finally, while I would recommend using high quality IC between the preamp and the basic amp, I don't think you need an IC of as high quality between the preamp and the subwoofer, given the nature of the signal. A Y cable would presumably be the same for both its legs; you could save money on the subwoofer leg if you used a splitter. Best of luck!