In some places the limitation is for insurance, they're insured for a certain number of people so if something happens that the hotel is responsible for (fire, building collapse etc) you're screwed and won't be entitled for the insurance if you fit more people in.

In almost all cases including in Malaysia, fire/bomba rules also play a role. Safety requires that the corridors and fire escapes be wide enough for x number of people so if more fit in the rooms then there may not be enough safe space when you have to evacuate.

In general though fitting 3 people in a 2-person room isn't such a big deal. 6... ?