OK. I'm working on a design. But I have more questions. Since you're so good at answering them!
Do you have any prototyping capabilities? Could you assemble a prototype on breadboard and play around with some component values?
I'm a bit unsure about what you want in terms of LEDs. I guess you want to couple them to the shell somehow, so the whole thing appears to glow? I don't know anything about how to do that. You could buy a selection of LEDs, illuminate them (see
https://www.electronicspoint.com/resources/got-a-question-about-driving-leds.5/) and experiment to see how many you need, how much current you need to run them at (determines their brightness), and how best to couple the light into the shell.
Be aware that LEDs are available in various viewing angles. Ones in clear packages have a bright light but a narrow viewing angle. Ones in "diffused" packages are the opposite. I would try both types.
I'm assuming this is for some kind of prop for a performance... Will it be used under lighting? If so, it will need to glow pretty brightly.
SMT isn't necessarily more expensive than THT; it just requires more careful assembly. I guess you plan to assemble the board yourself? I can use only SMT components that can be (carefully) hand-soldered. Would that be OK? It could save quite a lot of space.
For the microphone, I like the look of these little MEMS microphones:
http://www.digikey.com/product-detail/en/SPU0410HR5H-PB/423-1138-1-ND/2420982 but they aren't leaded. They are designed to be placed directly onto a PCB with blobs of solder paste, and passed through a reflow oven that melts the solder paste to form the connections and mounting. You could (carefully) hand-solder them slightly above the PCB using short wires or pins. What do you think?
How many of these are you making?
What do you mean by "flicker or fade"? The design I'm working on would fade the LED up smoothly while it detects continuous sound, and when the sound stops, the LED would fade out slowly. No flickering involved. Does this sound like what you want?
What is your electronics experience?
Edit: How many CR2032s could you fit into the shell? You'll probably need one for every LED, plus one or two for the circuitry.
Edit2: Have a look at Lithium Thionyl Chloride (LiSOCl2) cells. If you can find a US manufacturer of a suitably small cell, they might be a good option. Each cell is about 3.6V so you would probably need one for every 1.5 LEDs plus one for the circuitry. Their advantage over standard lithium coin cells is their lower internal resistance, which means they can deliver higher current without voltage droop.