The interior of the bubbles is mostly steam. When you raise the lid, cold (well, below $100^\circ\text{C}$) air flows in and the steam in the bubbles condenses and collapses the bubbles.
I don't know of anyone who has done the experiment, but you should find if you lift the lid when the outside temperature is $100^\circ\text{C}$ or greater, the foam will not collapse, or at least it will collapse more slowly. Presumably you'd still get evaporation from the foam surface.
Edit: just out of curiosity I worked out how much air would have to enter the pan to condense the steam in the foam.
Density of steam at atmospheric pressure $\rho_s = 5.90\times10^{-4}\text{ g}/\text{cm}^3.$
Latent heat of steam at atmospheric pressure $= 2.26\text{ kJ}/\text g \implies 0.00133\text{ kJ}/\text{cm}^3$
Suppose your pan contains $100\text{ cm}^3$ of steam in the foam then the heat given off when you condense it to water at $100^\circ\text{C}$ is $0.133\text{ kJ}$.
The specific heat of air is about $1\text{ J}/(\text{g}\cdot\text{K})$ so assuming the air in your kitchen is about $20^\circ \text C$, i.e. a temperature change of $80^\circ\text C$ when it hits the steam, you need $1.66\text{ g}$ of air. The density of air is about 1.2 g/litre so you need about 1.4 litres of air to fully condense the steam. I must admit that this seems a lot.
However you probably don't have to condense all the steam to collapse the foam. I suspect (but can't prove) that condensing the steam just inside the bubble wall would be enough to destabilise it and cause the bubble to break. The remainder of the steam in the bubble would simply escape and wouldn't need to be condensed, so the volume of air needed would be greatly reduced. Still, I have to concede that evaporation could well be an important factor.
Two reasons:
the cheese has a higher specific heat capacity than the crust;
the cheese has a higher thermal conductivity than the crust.
When you cool a given weight of cheese or crust from the oven temperature to your mouth temperature, the amount of heat it gives up depends on its specific heat. So the cheese, with its high specific heat, gives up more heat than the crust and hence heats your mouth more. The cheese also conducts heat better so it can deliver the heat to your mouth more quickly, and again this makes your mouth hotter.
All of which is fine, but actually it may simply be that the crust cools faster than the cheese while the pizza is sitting on your plate. I can't say if this is the case because I've never done the experiment!
Best Answer
The holes allow the steam created to be released gradually.
If they were not put in there would be a possibility of a sudden messy explosion, or someone getting burned by a sudden release of steam when they opened the lid.
Why your food didn't seems as hot might need more 'experiments' to decide.
Microwave ovens create hot and cold spots in the food, the heat then disperses. Perhaps by chance you eat some from a colder area than before.