Desktop clients are indeed the better option as you have full control over every aspect of your coins, but that's assuming you run on a clean cumputer with the required security measures. It's not that when you make use of a desktop client that you automatically enjoy a high level of security. It's as safe as you want it to be. That's why it's important to secure all your wallet files with lengthy passphrases. On top of that you can add an extra layer of protection by encrypting your wallet files
That would really add nothing to security
Your private key is still held in memory unencrypted for some time (I don't even mention keyloggers), so if your computer gets compromised, most likely you can kiss your coins good-bye. Even if you run Linux in an unprivileged environment, there are exploits that allow the attacker to get root access (if you use unpatched kernel). Once I did that myself on my own Linux box for test purposes. I found an exploit for my version of kernel, it was just a few lines of bash code, and voila, I got root access from an unprivileged account. And with root access (administrative access in case of Windows) you can do pretty much anything (e.g. read any segment of memory)
If you took the effort to thoroughly read through my post, then you would have noticed that I stated "that's assuming you run on a clean cumputer". So yes, it does add plenty to the security of your private keys. Paranoid people can even choose to run a seperate system solely for the purpose of syncing and transacting through their desktop client.
Cumputer?! What did I miss?
Nevertheless, if you read my reply carefully, you would certainly see that I specifically mentioned "if your computer gets compromised". That pretty much accounts for your assumption and basically means that even if you run or create your wallets as well as encrypt them (or do some other black magic) on a clean box, this doesn't in the least prevent your computer from the possibility of being compromised any moment (I'm afraid even to imagine what might happen to a "cumputer" in this regard). You should understand that as long as your desktop or notebook is connected to Internet, you are in a red-light district, so to speak
Computer as in PC or notebook or whatever other name label you want to stick on it. Yes, whatever you do when you're connected to the internet there is always a possibility of having your connection/system compromised. That's why you at all times should perform a thorough system checkup before you copy your digital wallet files or private keys into the client you are running. But it basically only applies to people having a decent level of understanding regarding their OS. The average Bitcoiner won't go through all of this aside from the standard antivirus to scan their system.