No, I don’t think there are major scientific discoveries that are being kept secret, but there are definitely discoveries that don’t get written about, or aren’t published, or that people don’t know about because they don’t read the right papers.
A good example is Konrad Zuse whose Breadth First Search algorithm is fundamental to how modern computer networks work. His PhD thesis about BFS was rejected in 1945. The algorithm was reinvented by Edward F. Moore in the 1950s and only applied to computer networks in the 1960s by C. Y. Lee. Now it is one of the most important algorithms in computer science, but it was 15 years before anyone realised how useful it was.