Personally, I feel that alliances also should count, especially if the diplomacy gets tweaked enough to work more stably than it currently does. And I don't think it should be military scoring only, tech, resources, shipyard capacity, trade and so on are very much a part of a nation's power. If there were no non-military routes to victory, sure, firepower and ships alone would count for the score. But as long as this is an empire building game as much as a military one, empire building needs to be rewarded.
On the mothballing issue, yes you "can" unmothball ships... if you have enough resources to do so. Most people mothball because they're running low on resources or are tight. I've played against people who had three or four times as many ships mothballed as they could afford to return to service, had they started unmothballing, thier income would have gone negative. Those ships ought not have counted for much on thier score. Now they could, and did, unmothball a few at a time and go and get them killed in battle freeing up economic space to unmothball a few more, and so forth, making unmothballing cheaper and faster than building equivalent fleets, so even in a case like this they should be getting something as the ships were indeed working to protect thier territory. But they oughtn't get full value for the ships.
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