no apps listed in my mac's microphone privacy setting after updated to mojave

First I would try booting in Safe Mode then restart normally to see if the list repopulates. If not post back.

Use safe mode to isolate issues with your Mac - Apple Support

Completely uninstall cleanmymac - this is to be considered malware.

Then run the 10.14.4 Combo Update, to try and fix the stuff that cmm corrupted.

See how things go.

Ultimately, a clean install is probably the way to go, but try the above first.

Never let this **** of a program anywhere near your mac.

One should never use any program that claims to "clean", "speed up" or "optimize" your mac. They're scams.

This one is particularly nasty.

You should run Etrecheck again and make sure that there are no remnants of this still around.

The comprehensive solution:

1) Make a full backup of your mac, preferably two

2) Erase your drive and install Mojave

3) Migrate ONLY the user accounts; NOT applications, settings, or other files.

4) Install from the App Store or the respective developers' sites the applications you want to use.

You will end up with what may seem like a new mac.

Start an application that would use your microphone - for example, start Quicktime Player and try to do a sound recording.

Do you not get asked for permission?

Please run EtreCheck and paste the report for analysis.

http://etrecheck.com/

Use the additional text icon under the reply window to paste it in.