yes I do use multiple wallets right now because its just bit safer than normal, if you spread your bitcoins in different wallets its safer so if you wallet get hacked they will only steal a small amount of bitcoins.
Its just a sort of security measurement to be sure your bitcoins are secure and safe.
if a hacker steals your wallet file and manages to access your coins, then it means that you secured your wallet file with a weak password, or maybe you didn't had a password at all. always make sure you use long passwords with random symbols to secure your wallet files. that way a hacker won't be able to steal your coins when they have your wallet files.
what ever password you put, if the hacker hack your computer and steal the passphrase of your desktop wallet then you can do nothing, So it is upto you that where you keep your wallet,
I am using both desktop wallet and online web wallet, desktop wallet for investment that i use it only for storing my Bitcoins for future expenses, and i keep that wallet in a pendrive and when ever i am in need i use it on clean computer and as soon as my work finish i just uninstall after taking backup in pendrive. That way i am secure
Web wallet i am using for my daily work as i am using coinbase and their security level is very good, as soon as anyone uses my wallet on new ip they will first check with sms code and after that email confirmation, so in this two way i am fully secure.