Yup. two caveats. The first being that you want to keep backups of your wallet.dat. With two clients running (each with its own wallet) make sure to have some way of identifying which wallet is which (e.g. if backup up to a flash drive, make a unique folder name for both computer A and computer B).
The second ... if your wallet had Bitcoin addresses that were used (i.e., received a payment) prior to performing the passphrase encryption step then you may want to spend those funds (to a new address, even if in the same wallet) so that you have no funds remaining in any Bitcoin addresses that were in use prior to when you did the encrypt step.
For instance, if you have an old backup of the wallet.dat and then you protect your wallet with Bitcoin-Qt's passphrase encryption, the keys in that old backup are still unencrypted and could be used to create a spend transaction. But as soon as those funds are spent you no longer need to worry about that old wallet.dat floating around somewhere.
[Edit: Incidentally, I see a Question on StackExchange for this topic as well:
How can I tell if my Bitcoin-Qt wallet is protected with encryption?
- http://bitcoin.stackexchange.com/questions/8125 ]