I have no idea why it's doing this and I need help as I'm a complete noob when it comes to configuring these things.
Thanks!
It only started happening once I enabled the mod

As there is no config that states that weapons will have ammunition. you have to go through the data loottable and add arrows.wood (or whatever) to each barrel or chest and ensure that you have the minimum amount set to ensure that there is a chance to get both ammo and weapon, apart from that they are easy to craft as basic ones dont need a workbench, high velocity and fire arrows need workbench one,
Remember that as it is a data file the plugin has to be unloaded (or server off) when you edit, save THEN reload the plugin and the best results are achieved if you use a json.validator to check the file before you reload the plugin , if you miss one comma or bracket it will revert to default (last saved) config