1. When clicking on a transaction to get details, the from field always shows 'unknown', though the information is certainly obtainable and is listed in the block explorer.
Yeah that should be easy to fix, but small Qt issues like that are not high on our list of priorities. We may still ditch Qt in favor of an RPC based wallet.
2. In payment requests, the balloon for the message field states that the message will appear when opened by the recipient's client but will not be sent with the payment. This does not appear to be true since I can't see where it's encoded.
The balloon text is from Bitcoin but it should still apply to Cryptonite. That payment request stuff creates a cryptonite URI, but you are right it doesn't appear to encode the message in the URI. I think that bug probably exists in bitcoin too.
Also, why wouldn't it auto fill the message field in the recipient's payment screen? It could be useful for returning confirmation codes to prove a particular customer has a payment.
Well I guess it's supposed to be a message from the payee to the payer, not necessarily something that the payee wants to have included in the transaction. But you are right it could be useful as a way to verify payments from specific customers.
However, wouldn't it also be better if the message was encrypted so that only the payment recipient could read it?
The payment recipient (aka payee) is the one who created the URI in the first place, why would he/she want to send an encrypted message to themselves? If you're simply asking why can't the messages be encrypted, of course they can if the payer knows the full public key of the payee then he/she can encrypt the message using that public key, meaning only the payee with the private key can decrypt it. But the payer can only get the full public key if it has been used to sign transactions in the past or if it's given to the payer by the payee.
One last one, There doesn't seem to be any qr codes. They're intended to be added to the next release right?
I believe that's just because the build you're using doesn't have those features enabled. You need to have the libqrencode library installed when building to make the QR code stuff work.