HTML5 games have viewable source code. Is there a way to make them like swf files?
Yeah, use Flash and translate your code to ActionScript.
How would one go about hiding the game algorithms?
In absolute terms, you can't do that.
What do you think of the Firefox JavaScript Deobfuscator Plugin and obfuscation?
Obfuscation is nothing but a very thin barrier for somebody who'd be serious about stealing your code. Still, it's simple to setup, it can repulse the most dumb script kiddies, and it's the only thing you can do to protect client-side code. It has the additional benefit that it reduces the script size (faster download) and can even optimize the code (faster execution). Check this entrythis entry on Stack Overflow for details on obfuscation. Summary: you have plenty of options. I personally tried UglifyJS and had very satisfactory results.