It depends. The main reasons C++ code can be slow are costly abstractions (don't laugh!), inappropriate data structures, and pointer fest (that leads to cache misses).

Writing the same program in JavaScript won't change much of the above. You'll have the JIT overhead for sure, but the basic data structures will remain relatively efficient, and if you're starting out with a pointer fest it won't be any worse in JavaScript. As for the GUI itself, well… I expect it'll be as fast as any browser.