is there a way to make these not take damage will true pve.

I believe there are other plugins that can help you make it so the pipes won't take damage. They are just walls so plugins that make bases invincible should make the pipes invincible.

I'm running into this issue as well. Had the same problem with JPipes. I think it's the Owner coming back as Unknown. So since it doesn't belong to a "player" per say, damage is allowed? It does come back as a Prefab so maybe set that in one of the flags? I'll test that right now

Merged post

So with JPipes he told me to search for this in the .cs file which I did and it worked but currently JPipes is broken. Tried searching for this in SyncPipes but didn't find it. 

if (entity.OwnerID == player.userID || entity.OwnerID == 0)
{
    return true; // allow damage to entities that the player owns
}​