Reading a plot summary of Thirteen Ghosts it seems like the ghosts are trapped by inscriptions written on the glass, so there is nothing specifically important about the glass rooms (please correct). There is no indication in The Cabin in the Woods that the glass rooms had a similar confinement - the use of glass seems unimportant - perhaps other confinement is required for the non-corporeal residents of the facility.
The Cabin in the Woods deliberately pulls on all sorts of standard tropes about horror movies and government conspiracy. Rather than being inspired by the glass rooms from Thirteen Ghosts, it seems like The Cabin in the Woods is rather more inspired by the trope of 'secret government facility' with aliens or monsters held in confinement, usually in glass rooms. As an example of this trope, Monsters v Aliens has such a facility, with most of the monsters kept in glass cells in a very similar arrangements to The Cabin in the Woods.
As TylerShads indicates in his comment - there are many references to other horror stories in the movie, the whole point of the story is to imply that there is some sort of reasoning behind horror cliches. It may be a 'nod towards Thirteen Ghosts, but inspired would perhaps taking it too far.