Looking at this purely from a business standpoint, I think Ares' took a big gamble going with 1:1000 scale, but it has paid off handsomely, and may pay off even more handsomely going forward. I don't mean to second guess their choice, but I like these little mental exercises. Feel free to ignore my musings...
If Ares had stuck with 1:1200 (putting aside any manufacturing issues. It wouldn't surprise me if plastic ships at that scale would have several QC issues, although I'm no expert on that topic), the pressure would have been high for them to alter their production schedule dramatically. Owners of existing 1:1200 scale ships would demand the necessary gameplay elements (ships cards, ship logs, and perhaps ship bases) to use their own models. Ares may or may not have responded to that pressure, but I think selling just the cards/logs would be disastrous for Ares in the long run. Here's why:
1. As we already can see from other games like WoG, X-Wing, Star Trek Attack Wing, etc., there is a practical and financial limit to how many ships a company can produce at once. So they are sold in "waves". The limits of producing ship models don't apply to producing cardboard ship logs and ship cards, though. The necessary capital and manpower to produce them is WAY lower.
So what if they produce ship cards/logs/bases for existing historical ships for gamers who already have lots of ship models in their collection - even before Ares is able to produce the corresponding models to go with them? Their profit margin would go down (cardboard pieces don't sell for as much as the ship models), and there would be a risk of alienating new players who would want to play with these new "ships" but don't have the models with which to play them (and lets face it - completionism is rampant among gamers, so this isn't all that speculative). This invites competitors to start producing ship models to compete with Ares' own ships - and what's to stop them, if Ares' is essentially inviting players to use third-party ships to play SoG by producing the cards/logs/bases?
2. Alternatively, what if they only release ship cards/logs/bases for separate purchase as the same time as they release their own models? This potentially alienates players like Rory (sorry Rory - you are just the stand-in example!), who wonder why Ares is "preventing" them from using their own Langton's models. We "know" that it's easy-peasy for them to publish the ship cards/logs/bases for dozens of ships right away because the cost to produce them is so low (relatively speaking). And as discussed above, selling the cards/logs/bases is necessarily cutting their own profits. Third parties can freely sell their own 1:1200 scale ships (whether it's top of the line Langton's or lower end plastic knockoffs) and market them to SoG players knowing that Ares is providing the necessary materials to use these ships in their game. Why should Ares allow competition an even playing field?
3. Ares can decide NOT to produce ship cards/logs for separate purchase than their models, so that they don't give third party competitors an even playing field. The difference in scale is not so large that players can't still use the 1:1200 ships mixed in with 1:1000 scale ships, as it is the ship's base that is important from a rule perspective. Yes, the difference in scale is likely noticeable to a casual observer, but not so large that it takes away from the gameplay. So if hobbyists want to use their own ships, they can jury-rig (sorry, couldn't help myself!) their own cards/logs to use their own ships.
But then, if players are jury-rigging their game to include their own ships, why should Ares' bother at keeping the models at 1:1200 anyway? Especially if there are manufacturing issues that makes it more practical for Ares to use the larger scale? So then we are back to where we started.
I'm no expert, but it seems to me that there are a lot of potential downsides to Ares producing ships in the 1:1200 scale, with few corresponding upsides to them. Yes, it's nice for those hobbyists who already own lots of 1:1200 scale ships and don't want to be inconvenienced with a slight size disparity when they use them alongside the "official" SoG ships. But as Gunner pointed out - the easiest road to failure is to try to please everyone.
The one argument I see in favor of Ares publishing at the 1:1200 scale is that they could plan on the ruleset and starter game to be their profit center. The idea being that allowing (encouraging?) third party competitors to make ships usable with the base game will tend to encourage sales of the starter set - something analogous to Microsoft making Windows hardware agnostic - as long as everyone used Windows, they didn't care who actually sold the hardware. But the response to this argument is pretty obvious - the potential market for SoG is extremely limited. Even with the unexpected success of SoG, sales will never reach into the millions of units. It's just too much of a "niche" game. So Ares has to maximize their ability to sell every component to be used with SoG because the profit margin is so small (relatively speaking). Thus, 1:1000 scale is pretty much the right call, IMHO.
Okay, enough of my ramblings. Time to play with little sailing ships!