No issue here, just a question

Yeah that's a good question - I made the hatches indestructible mostly to make raids more interesting. If they were destructible, and were locked, then the raider would have to destroy the hatch to get past the lock. But unlike a regular door, if the hatch is destroyed, its now impossible to enter. So instead, the hatch is indestructible, but the locks on the hatches can be destroyed. In addition, the foundation that the (surface) hatch is on is still destructible. 

To answer your question, the only official way you can "remove" a hatch is if you were to demolish or destroy the foundation below it. I felt that in vanilla, buildings are quite permanent and difficult to rearrange, so it made sense for basements to work that way too. However, as you know, there's many plugins out there that provide convenient ways to remove buildings (RemoverTool, BuildTools, ect) and I have recently made it so that those work with the hatches. I didn't want to reinvent the wheel and include a remover tool just for this plugin, if that makes sense.

No problem!

Changed Status from Pending to Not a Bug