I don't know either, but I can speculate that as a small company it's not worth the financial complications to produce more than is needed for the kickstarter (+defects) and then manage sales. Also the whole deal with supporting the kickstarter was getting the physical version. It's that same thing that drives people to go bananas over even mediocre games offered by LimitedRunGames. So this taps into some of that purchasing fever that surrounds limited produced games as I'm sure a lot of people supported this even if they weren't big fans of the genre. Violating that group of people by offering the physical stuff after the KS is not a good deal when the next project comes along. So it's kind of in their best interest not to produce more physical copies if they want to make more games. Especially if that dilutes the market such that they have to sell them at a loss because availability isn't an issue. Oh and availability is such a huge component of the market these oddball Vita games revolve around. I mean, they could produce another batch of any of the existing rare vita games but once the games are no longer rare the stock is just going to sit there while the price drops because as many collectors as there may be for physical Vita games... it's not that massive a market. Look how quickly things drop to $20 and even $15 now for even some recent releases. It's a massive gamble because the demand is going to be super questionable and a lot of vita gamers have no problem waiting on a sale when the purchase is only going to pad their collection.
Plus they already have a built in ongoing money stream for MuvLuv by making the games digital as well. So physical isn't the only option to play the games and for a lot of developers getting something made physical is an amazing achievement but ultimately they want people to play the games they make which for something like a VN where the market here isn't that huge... digital makes more sense as most likely the prices will have to be good anyway to attract random purchasers and they won't have to pay for and manage any inventory and sales.
But I've kind of had the same sense of bewilderment towards this stuff. Especially the LRG games when it seems they could sell an extra few thousand copies without an issue but they settle for making less money because they are dedicated to not just making a one run game... but cutting the numbers short to ensure it's limited. In the end they are taking a gamble by producing a fixed amount and vowing never to make more... but the end result is that vow also costs them a lot of potential money as scalpers are going to eat up a lot of that market because it's almost a sure thing that the games (regardless of quality) will sell for much more than was paid because they are so under produced. So regardless of what they do to limit purchases... people find ways to work around it and it even tempts regular gamers to buy with the intent to sell.
So sure MuvLuv could be done in a limted batch... but I think ultimately they did give everyone a lot of time to decide if they wanted a physical copy anyway without some miniature limited amount. For anyone that missed it, they can at least still buy the games as they come out digital... I mean if they actually want to play the games... or just pay the scalpers as I'm sure a lot of these physical games will end up being resold once they start showing up in mailboxes.