First of all, did you check your downloads list in the Playstation Store app, and the Account Management app? Even if the game is no longer available for sale in the Playstation Store, it may still be available for download by previous purchasers. Licensed games are usually only available for sale for a limited time, because the IP license is usually granted to the developer or publisher for only a few years. The exception is when the game developer, and the license, are owned by the same company; Disney, or LucasArts, for example. That said, if you read the Playstation Store terms of service, it clearly states that content can be removed from the Playstation Store at any time, without notice, whether you purchased it or not. Legally Sony only guarantees that the game will be available for you to download even the first time, if you download it immediately after purchase. Any later than that, and all bets are off. You are not guaranteed access to the game for any specific length of time when you buy it in the Playstation Store.
While space on the Vita memory card is limited, the Vita Content Manager can back up games to a Windows or Mac PC, in addition to a PS3. You don't have to rely on being able to download the content from the Playstation Store, and in fact you never could rely on that. A PS3's hard disk drive can be upgraded to 1TB or more, so there is space for all of your Playstation Store games; and downloaded games can be backed up to a USB external hard drive; although that won't help if you get the YLOD, because games won't be restored to a different console.
There is no way to ensure indefinite access to Playstation Store purchases, and there isn't intended to be. You don't own anything when you buy something in the Playstation Store. It is more like an indefinite-term rental. What you are buying is a license to use the content, and the license ends whenever Sony says that it ends. You have no say in the matter. When it is gone, it is gone. Enjoy it while you can. Fates/Unlimited Codes was only available on PSN in North America, so you had no other choice about how to buy it; but the lack of ownership of even the copy of the software that you purchased is one of the key differences between buying a game on a disk or game card, and buying a digital download. One you get to keep as long as you want, and the other you don't.