Ah, so someone had already asked them directly about a physical Vita cartridge. Just found this at the bottom of the KickStarter page.
Quote:
Will there be a physical release of the PS VITA port?
?A physical release of the VITA port isn't planned as of yet, but expressing interest in one is a huge support. Before promising anything, we should be realistic and see how the VITA game will do in the west first, as mass production of the chips may be costly. Above all, we don’t want to overcommit and jeopardize our ability to successfully bring Muv-Luv to western audiences.
?If you have further concerns let us know and we'll update this part of the FAQ. 
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The good news I read here is that they have not said "no" to doing a physical Vita release. Additionally, the highest tier goal for this KickStarter campaign is only set for $720,000. So, it is entirely possible that if enough of us message in asking them for it that they could set a new goal tier to fund a physical Vita release of this game trilogy, which would be great!