Many craft carry specialized equipment that is used throughout the mission
Your mission equipment will vary considerably with the purpose of your spacecraft. For a warship you have to factor in the mass of missiles, cannons, and ammunition. You also have to account for the mass of the launchers and the sensor equipment that detects the enemy. If the equipment requires live human operators, you have to add a station to your command center, which takes up volume. Your equipment is also going to need power.
The quickest way to estimate all of this is to figure out the volume, and then approximate back to the mass. A rack that is 1 cubic meter in area probably has a density of steel for the solid parts (8000 kg/m^3). But inside the rack it is probably mostly air (75%).
If the ship carries shuttlecraft, add the cost of the shuttle. And also figure on having some fraction (I recommend 25%) of that mass in spare parts and consumables.
Bulk CargoIf the ship carries cargo, work out the mass and volume of the expected cargo. If the ship is carrying some kind of ore, figure out the volume from the mass and density or the mass from the volume and density. For general purpose shipping, you can assume a density of around 1100 kg per m^3.