I might need some more info. Your config looks OK from what I can tell - it looks like you have it configured to only allow PVE players to attack NPC bases, which makes sense. In this case with PVE attacking PVE, I would not expect it to allow you to damage it. Initially, I think it might be one of the following issues:
The player who owns the base is PVE, but if they have even just ONE PVP player authed on it - it will be considered a PVP base. Even if this was the case though, you still shouldn't be allowed to damage a PVP base if you are PVE based on your config rules.
If you have another PVE plugin or any plugin that has logic to block damage (like TruePVE for example) its very possible that it may be conflicting with WarMode. If so, you need to make sure you configure all PVE plugins to not interfere with each other.
There could be a bug - perhaps FacePunch changed the way explosive damage works and it may require a fix. I will see if I can rule this out.