As with all design decisions, it's a trade off. The main benefit of web apps is found in their cross-platform nature. If this is desirable then you may choose to sacrifice a little performance to get that.

To give an analogy, it's like programming languages. It's possible to write very fast code with assembly languages, yet their portability to other architectures is practically non-existent. Part of the reason higher level languages like C/C++ are used is because they are much more portable.