In practice it doesn't seem to matter. For example btc-e.com who accepts both bitcoin and litecoin for trading makes you wait 3 confirmations for bitcoin and 6 confirmations for litecoin. So you are correct that 1 litecoin transaction is not as reliable as 1 bitcoin transaction but they are not making you wait 12 litecoin transactions.

Given that btc-e has a lot to lose on double spend attacks I think it's a good measure of how these two currencies are playing out in the market.