Oh, my bad. The door is set to owner only permeneantly. There's lots of ways to get through blocks. Commence questioning.
Did he use a portable hole?
Are you sure you know what's in his inventory?
Does he run the server?
Does he like sheep?
Is he secretly in contact with any mods?
Does he have hacks?
Are there any warded glass windows in there?
Is it possible that he simply stood there with an efficiency 5 thaumium pickaxe and sat for about 20 minutes mining away at two of the arcane blocks, then replaced them afterwards with his own? (Arcane blocks take 3x longer than obsidian to break, so it's still possible to break them even though you'll probably be in the mood to murder somebody if you let go of your left mouse button).
To check the previous statement, mine and replace EVERY arcane block in your base.
Do pistons move warded stone?
Are there any two-way teleporters in your house?
Is it solar powered? (If so, then he probably broke a hole in the solar panels and mined through the wiring to get into your base)
Are there any piston doors that are protected by warded stone?
Did he get TPed by one of the mods?
All of these are just random guesses on the spot, FYI. I may go into my singleplayer world, and test ways to get past warded stone. (Besides breaking it)
Did he use an invisibility potion to sneak in behind you?
Did he use Modular Power Armor to get an invisible set of armor and sneak in?