You don't get it-- the positions are not vacant, and they can't be vacant unless Congress abolishes the position.
By law, someone must be, say, the Assistant Secretary of State for East Asian Affairs (one of the positions Trump hasn't nominated anyone to). So the office is either being held by an Obama-appointed holdover or, if Trump fires the holdover, the longest-tenured civil servant in the office becomes the Acting Assistant Secretary.
The position is not "unfilled," it's being filled by an ideological enemy of the President.
I see your point, but ... If the AG resigns and the Deputy AG takes over indefinitely, then the head count for the DOJ is reduced by one — right? Because the Deputy AG would have been there anyway.