There are numerous downsides to storing coins in the client program though. I think it's more about weighing the up / downsides of each type of wallet and using whichever comes out best. Personally I think that paper wallets are the best as the potential downsides are fire and theft and I doubt anyone would know I had any crypto-currency. But with LTC you don't have that option so I was dubious about using the application which is vulnerable to Malware.