Yeah, it does seem unlikely that they are corrupted, it has happened before though, admittedly, I don't think they were in zipped format then.
Yup, the old .pcx files that came with the original Freespace used pure Green to denote transparency, they still work, but things like shockwave used to be additive textures, which meant that their colour value was 'added' to whatever was there, so bloack was transparent, that's changed now to using the Alpha map of the texture, so turning off jpgtga will make Freespace revert to the old .pcx files for the weapons, which work, but the shockwave, I suspect, is still using the .dds file without an alpha map, which is why you get those big black areas.