If you plan on making a long-term backup, for the purpose of safeguard against data loss, after encrypting with a passphrase, you might consider starting Bitcoin once with a large keypool option such as bitcoin-qt -keypool=2000. This will fill the wallet with future keys that will keep your backup from becoming obsolete for a long time.
Good idea. Do I change it in the shortcut properties, or somewhere within the program itself?
Neither since you only need to set it once. In windows the easiest way is probably use the command prompt and type the command exactly as shown above. Once the keypool is set loading it in the future won't unset it so there is no need to add it to a shortcut. Understand it can take a while to generate a large number of keys and there will be no progress indicated by the system so just be patient eventually once the keypool is expanded the client will load normally.
Another question: If I kept my wallet in cold storage, and I deposit more coins to a known address in that cold storage wallet, does that change the number of keys in use? How would that affect the existing unused keypool?
It wouldn't use a new address thus it won't change the number of available keys in the keypool.