I never encountered one single Monster House on my way to Rayquaza, just stay away from wide open spaces. If you do encounter one, just give it your all with your linked attacks.
Get the item X-Ray Specs.
Give it to your leading pokemon.
In Monter Houses, there are usually a lot of items.
If you see multiple items near each other, that room might be a Monster House.
That's the way I locate Monster Houses(but I actually like them, and I go to them)