The answer would depend on the structure of the thesis, i.e. whether it is a series of essays (often known as "three essay format" or a single integrated work with specialized chapters. In the former case, by all means it is relevant and indeed necessary to have literature review and methodology sections within each chapter/paper. In the latter case, there should be separate chapters for literature review and methodology.
1. Is this "three essay format" is common or valid in Computer science thesis?
2. Whether it creates the problem of linkage between chapters, when we have literature survey in all the chapters? If yes, please suggest for linking chapters?