Take block #270632. This includes a fairly typical 469 transactions, and gets 25 BTC reward (13949.34 USD according to CoinMill). They only took 0.14727399 BTC (82.17 USD) in fees. Basically, they received an extra 0.58% in reward fees. Bitcoin price has dropped by 1.07% (src: Bitstamp - Open 536.01, Close - 530.25) today alone. Does 0.58% extra really justify killing the performance and usability of Bitcoin?
I doesn't kill anything. It just takes a little longer. Paying a few USD cent gets rid of the wait time. It's everyone's choice what to do. Personally, I don't think twice about those few cents. And on top of that, I know that those few cents even go towards improving the network (in a tiny way).
That's why it is good practice to wait for 7 confirmations before accepting a balance.
How? The stock Bitcoin Daemon certainly doesn't discriminate between confirmed and unconfirmed. It just seems to pick appropriately valued outputs to use as inputs - regardless if they are confirmed or not. Literally; "bitcoind sendtoaddress {ADDRESS} {VALUE}". There is no choice.
If you are the receiver of a transaction, you only accept it as valid if it has 7 transactions. Mind, this is only for high value transactions. It is unlikely that someone tries to double spend small amounts, so merchants often accept transactions that were just broadcast to the network and have not even been included in a block.
Or are you asking how to see how many confirmations a transactions has? Your client should show you. You could also use
https://blockchain.info/address/.