Also minecraft is java if I'm not mistaken, not javascript.
Kyatric is right, Minecraft is written in Java not Javascript. Java is more comparable to C++ as a language, and almost as fast, so you can't really compare Java's performance to Javascript.
Performance is a complicated thing. Whether or not hardware acceleration is enabled depends on a number of factors, including the browser version, the OS, your actual hardware, your driver version, and so on. Hardware acceleration is never guaranteed to be enabled - Firefox 6 doesn't like my old GeForce Go 7600, so disabled hardware acceleration even with the latest drivers. However, IE9 (of course, not available on XP...) doesn't mind and still used hardware acceleration. Worse, it's often hard to tell, since FPS rates vary and browsers have a number of places hardware acceleration can be used, e.g. in rendering ordinary HTML documents, but not covering the canvas element itself!
To further complicate it, different browsers, systems and hardware have different performance characteristics - regardless of whether hardware acceleration is enabled, different systems can still get very different framerates, because they're good at different things. And by "system" I mean the entire system from your physical graphics card right the way up to the browser software version.
TL;DR - when it comes to performance don't expect anything. Maybe try some different browsers and stick to whatever works best for you.