In 99% of other altcoins, the block reward is sort of "minted" when the block is solved, the coins aren't sourced from anywhere, there is no input. However, unlike all those other altcoins, Cryptonite has a concept of balances, that is what the trie.dat file is, it's a list of all non-empty addresses in the network and their balances. The inputs and outputs simply point to addresses in that balance sheet, instead of pointing to other transactions as they do in most other altcoins.

When a block is mined in Cryptonite, the block reward is actually subtracted from the balance of the coinbase account, and that is why the transaction in the genesis block sends the total coin supply to the coinbase account. The address for the coinbase account does not have a known private key because it's derived from a public key hash consisting of all 0's. But even if the private key was discovered it still couldn't be used because it's only allowed to make coinbase transactions.

Since transactions don't have inputs and outputs which link together like in other altcoins, there is no reason to store old Cryptonite transactions. ALL transactions can be forgotten after some period of time (it's a week in Cryptonite), there is no reason we'll ever need to go back and find unspent outputs, because in some sense all Cryptonite transactions instantly become "spent" after they are applied to the balance sheet / account tree.