Hello Mr_Kopy,
The Mac App Store is just that - a store - nothing else. There is a "Purchases" tab that may or may not have you past purchases. But if you use different Apple IDs, or if the app is discontinued, then it will no longer be available in the Purchases tab.
It isn't commonly known, but you should archive all apps that you purchase from the Mac App Store. While you should also have a Time Machine backup, that is a backup, not an archive. Your archive should be separate. Ideally, you should compress your archived apps too. Otherwise, the Mac App Store might corrupt your archives.
Transmit is only $34 and can be purchased direct from Panic. In fact, the Panic website doesn't even mention the Mac App Store. A number of popular apps have recently left the Mac App Store, or been mysteriously kicked out by Apple.
However, if you did purchase Transmit from the Mac App Store, and don't want to buy a new license, you will have to continue to work with Apple to get your purchase re-instated. Again, it is just a store like any other. Ergo, did you save your receipt? Without it, you have no proof that you ever purchased it.