If you microwave leftover egg shells is the salmonella dead on the shells
Yes or no - it depends.

We need to look at the question from two different angles.


Microwaves don't kill pathogens, they create heat that can kill pathogens.
While it seems basically the same, the important difference is that microwaves heat water, not dry substances. If your egshells are dry, you can microwave them for a long time and they will remain cool. Now add to this the fact that while many salmonella bacteria die after a few hours on dry surfaces, some go into a "hibernating" form that remains viable for weeks, your microwaved dry shells remain mostly unchanged with regards to their infectious potential.
Microwaves do not heat evenly.
Microwaves are notorious for heating unevenly. They can create hot spots and cool spots during normal use. The former is one of the reasons why baby food manufacturers typically discourage parents to warm baby food in the microwave, the latter is actually linked to various salmonella outbreaks when users heated chicken meat or other leftovers in the microwave without making sure adequate temperatures were reached. [1], [2], [3]


So the conclusion:

You need to make sure there is enough water and enough time involved to kill your salmonella in a microwave. Consider the techniques used for pacifiers and similar baby items: A closed, microwave-safe container and a few tablespoons of water to generate plenty of steam, a minimum time of three minutes once the water boils. What's considered safe for a newborn should suffice for your eggshells, too.   

Personally would probably dump the shells in a pot of boiling water instead, if I wanted to be very sure. Or pop them in a hot oven after using it anyway, e.g. after baking bread or cake.