You can remove vehicles by not specifying a teleporter for them in their CFG entry. There are lines like UseWaterTeleporter TRUE and UseBigTeleporter TRUE. Change them to FALSE or remove them. Buildings cannot be removed, but you can give them an impossible dependency, like a level 5 Tool Store when it normally only has three levels. Check the Dependencies { section of the CFG. Consider also giving such buildings a 1x1 black pixel image (it sounds like you did this already). I'm not sure if the game will automatically align them, but you can place them at the end of the list. The order is defined in BuildingTypes {
You may want to adjust some of the sidebar interface images if you do that last thing, as you'll have empty spots in the list if you don't.