When I made a secret base on my old server, I made a very long skylight from my energy room to the surface and planted a dense forest around the hole. After the trees grew, I cleared out the leaves that would block the sunlight and then I was done. The only people who ever found my base were told it's location and shown the secret lake bed entrance. It was eventually greifed and destroyed, but only because I was too friendly and insisted all trades occurred at my base. Being the main supplier for the server (I knew all the (at the time) secret recipes), I was bound to accidently invite a greifer in at some point.