Not knowing the whole story, or even a good half of it, I can imagine, in the case of Egypt, that their tourist economy and their national identity are very closely tied to the integrity of the pyramids, the Sphinx, and other ancient relics that have already been explored, exploited, and have their history of abuse, as well as mishandling. These things would understandably leave them reluctant to allow any excavation that could possibly threaten their current trove of archeological attractions. The reports of newly discovered structures deep beneath the pyramids do not seem to be solid enough to risk a major dig so close to such fragile structures as the 5000 year old pyramids.
In the case of Göbekli Tepe, the stopping of excavation and the subsequent planting of orchards over the dig site is inconsistent with the other amazing archeological sites they have uncovered and opened up for tourist, of which three I have had the pleasure to visit. On the other hand, there may be concerns over aggressive activities along the Syrian and Georgian borders that make covering up, and even hiding the site a reasonable decision. It is certainly easy to come to any conclusion a conspiracy theorist wants, when a government spreads something so inexplicable and won't discuss their reasons truthfully. I honestly doubt there could be found anything at Göbekli Tepe that would change our historical narrative in a way that would threaten Islamic culture. I don't think they are tied to Creationism or even the biblical accuracy of Genesis.