If you changed the timy hull for, say, the Terran ship style, but were playing with the Drengin ship style, your change would not have shown up for you.
You can alter the available hull size by modding your miniaturization, or by changing the sizes of particular hulls. But you have to make sure that you are using the style of hull that you mod if you mod the hull size directly.
The actual hardpoints, which as Kryo said are the red arrows on the hulls for attaching components, can be increased in number with Kryo's Hull System Mod.
In case you're wondering, the Terran style ships are the ones using the S0_ prefix, while the Drengin ship style uses the prefix S3_.
S99_ is the prefix for a hull that is available to all races.
Have you read CariElf's modding guide?
WWW LinkIt is a great help to new modders.