I'm currently working on a top down shooter inspired by (among others) "Mercenaries: Playground of destruction". 

I want to give players as much freedom as possible when it comes to finding a playstyle. I've already added the possibilities to break windows or blow up walls to gain entry to a room/building. After destroying most of the walls, it makes sense to have the building collapse, which poses a problem.

Since this game uses a top down perspective, the roof is invisible. How can/should I let the player know he needs to leave a certain area before he's squashed by the falling ceiling? I'm thinking about shaking the walls that still stand and/or letting some debris fall from the ceiling using a particle system. Does anybody have any other good ideas?

Wall shaking and falling debris are appropriate and likely to look good, but you might want to increase obviousness with abstract symbols:

• flashing the collapsing area in a bright colour to show the exact danger zone
• floating text overlays (which can include an explicit countdown)
• arrows to suggest escape routes

I like the idea of a flashing indicator letting the play know if the danger.  But some sort of animation where the building foundation jiggles  or rotates back forth to indicate the danger.  

Sound effects could also play a part in the immersion