If you dig down deep enough, you can put a workbench underground and then cover it up with wood/stone floor. Trying to cover it with dirt will eventually see it destroyed, but, if you incorporate them into your base in such a way that they're under wood or stone, then they stay hidden while still giving the advantages of preventing monster spawns and a way to repair your base.
Once I get into stone, I will usually dig up enough room for a workbench and stonecutter, then cover them up under floors. Heck, I even use stone foundations for pathways and stick them under those. You can't see them, but when you equip your hammer, you can see the area of influence for them and stick more in as needed for spawn prevention/repairing.