I haven't read the Polyhedron issue in question, but given the way that D20 works I suggest one of the following.
1) Linear interoplation. If your new ship size is between two of the published ones, split the difference between the two and assign your ship that HP value. For example, if ship 1 is size 100 and 12 HP, ship 2 is size 1000 and 24 hp, and your ship is size 500 it should have 18HP.
2) Linear extrapolation. if your ship is slightly larger or smaller than the largest or smallest ship, just multiply the hp by the size difference. For example, your ship is size 1200, it would have 24 HP x 1.2 (1200/1000) or 29 HP.
3) Exponential extrapolation. If your ship is significantly larger or smaller than the example ships, multiply the HP by 4 for each size class larger. For example, ship 2 is size 1000 (Large) and your ship is size 10,000 (Huge), your ship would have 96 HP.
Materials. I'm not sure what materials are offered, but at a guess I'd add +3 to +5 HP per rank of stronger (or -3 to -5 for weaker) materials used. For example, wooden hulls are the standard, so an Iron hull would be +5 HP and an Adimantium hull would be +20HP.
A WAG. If I had more details, I'd provide better answers.