Please tell me is it possible that the site is written using java and the logic is written for example in C. If so then why and how it happens bundle?
You can, there are many options, from calls to native methods to the RMI.
If at all this is washed away and when ?
The meaning can be in two cases - when it is necessary to make some very complicated computation with CUDA, OpenCL, etc., or when the performance of C code much faster. But in the second case it is logical to optimize Java code.
In most of the tasks related to web and enterprise, this rental is not needed.