Are the sprites assigned to the negative values given a blank image, and if so why are there five different versions?
No, there are no blank images.
There are no sprites with negative indices anymore, full stop.
If I remember correctly all HWP ammo was given a bigSprite: value of -1 to prevent it from appearing during the equipment selection screen or when aliens assault a X-Com base.
Am I correct in my assumption that this has been replaced by the command "ignoreInBaseDefense: true".
They were not assigned any value before; and that's how it should stay.
Please do not use "bigSprite" for HWP ammo at all.
"ignoreInBaseDefense: true" is not needed for HWP ammo.
If it has, do I still need to assign the item a bigSprite: value to an item that is using the ignoreInBaseDefense: variable?
No, you didn't need to assign HWP ammo any bigSprite before, and you should also not do it now.