RE: 101 or 103 unused keys in the keypool: That's normal. Here's the sequence of events that causes it:
+ You do something that requests a new key from the keypool. Several things do that (including the 'getinfo' RPC call -- it requests a key from the keypool so it can report the keypoololdest time).
+ The keypool automatically adds new keys so there are always at least 100 (by default)
+ The something you did returns the key back to the keypool, so now there are 100+1
I tend to have 104 keys in my keypools, because I do a lot of 4-core CPU mining on testnet-in-a-box setups, and the 4 miner threads each grab a keypool key that is released when bitcoind quits.
RE: better backup: good idea. However, the keypool might not survive for much longer; they're likely to be replaced by Hierarchical Deterministic Wallets (see https://en.bitcoin.it/wiki/BIP_0032 ).