While everything is armed the greyed out icon for "re-arm all" shows a small grog icon instead of gold. However once you actually need to re arm due to being attacked it changes to gold. So I assume it's just some sort of bug and will disappear in time.
It's related to this issue: http://forum.plunderpirates.com/ind...ame-gate-re-arm-all-cost-during-upgrade.6911/ When there are currently-upgrading defences that can't be rearmed the game bugs and shows 0 grog to rearm instead of not showing the rearm option.