I'm still downloading the Blockchain (which is going to take ages). My question is, should available Bitcoins be updated straight away launching QT (before the blockchain finishes downloading)?
No, the wallet has no way of knowing if that total is actually correct until it has fully synced and validated all the transactions that are applicable to your wallet.
Currently the total is 0.0000000BTC available. What's interesting is that I can already see all the transactions and comparing in/out it looks like I should have some BTC left over. Do I just have to let the entire blockchain download before available BTC is refreshed?
Yes. What you are seeing is the historical transactions that were previously recorded in your wallet file. However, these can NOT be "trusted" until the wallet has synced the blockchain up to the point that those transactions were created and it has validated them to make sure they are all valid and confirmed etc.
Additionally, your wallet has no way of knowing if there were any transactions AFTER the ones you can see... until the full blockchain has been downloaded and validated. That is to say, you cannot be certain you are indeed looking at "all the transactions".