The microwave is too harsh an environment for this.
If you have a sous vide circulator, you can also pasteurize in-shell at 135 F (57 C) for for 75 minutes according to Douglas Baldwin's A Practical Guide to Sous Vide Cooking.
To pasteurize on the stove in the shell takes some care. You must bring the water up to 140 - 150 F (60 - 65 C) for 3 to 5 minutes to pasteurize them. You must not exceed 150 or you will begin to cook the egg. If the eggs are in the water as you heat it then they will closely match the temperature of the surrounding water. Just make sure they aren't resting on the bottom of the pan. If you want to be extra careful you can leave them in longer, as long as you don't let them get too hot.
Alternatively, since you're using them in egg nog, you can combine the eggs with the milk and heat this slowly on the stove until it reaches a temperature or 140-150 F, maintaining for 3-5 minutes.
First of all, it is extremely rare for the yolk of an egg to become contaminated if the egg is reasonably fresh. Contamination only tends to occur when the egg is quite old and the yolk membrane weakens. (Source)
Now, that said, egg yolks begin to set at a temperature of 62° C (144° F), and salmonella can be killed at temperatures as low as 59° C (138° F), so it actually is possible to "cook" the yolk sufficiently to kill any bacteria without letting it set, but you have a very small window to work with, so you need to be careful. If the temperature is even 1° too low, you'll just be encouraging the spread of more bacteria, and if it's even 1° too high, you'll ruin your recipe because the yolk will set.
Nevertheless, if you have a reliable, uniform heat source, you could attempt to heat the egg to 60-61° C for about 1 minute.
Unfortunately, you won't be able to use the technique used in other recipes - such as Bavarian cream - of simply using the residual heat of the other wet ingredients to cook the yolk sufficiently for safety while not allowing sufficient time to set. Dark chocolate is the most heat-resistant but will easily burn at temperatures significantly above 50° C (125° F). Mixing the chocolate with cream may raise this temperature slightly, and I admit to not being certain of the exact amount, but I'm pretty sure it won't get you up to the required 59° C - and it really actually needs to be much higher than that because the temperature must stay that high for several seconds after adding the eggs.
So my advice to you is to either:
- Pre-cook the yolks very carefully to a temperature just below 62° C (use a thermometer!); or
- Use very fresh eggs from a reliable source; or
- Don't eat mousse made with egg yolks, if you can't tolerate the (very low) risk.
Best Answer
The main rationale for the "room temperature rest" for homemade mayo is to kill off potential Salmonella in eggs. Most other ingredients in mayo recipes should not be contaminated with bacteria, so I can't imagine any benefit from the room temperature rest when using pasteurized eggs.
In fact, given that mayo will degrade faster at room temperature (in terms of flavor and quality), it would keep the mayo fresher for longer if you refrigerate immediately.