I completely destroyed an HQ base, and the map marker still shows on the map after reloading the plugin. Is this intended?

If you destroyed your own base then yeah its still your headquarter there.  You can put up a new TC in that same area if you'd like.  As an admin you can also remove one or all headquarters if you want to.  As a user you probably dont want to destroy your headquarter base since you wont get the ability to start another one.

Something's not right.

"ProtectionPercent": 90.0,
"ProtectionPercentMinimum": 10.0,
"ProtectionSlotsWithoutPenalty": 15.0,
"ProtectionPenaltyPercentPerSlot": 2.0
     0 slots = 100% - this should be 90%
     6 slots = 94% - this should be 90%
     15 slots = 76% - this should be 90%
     20 slots = 66% - this should be 80%

"ProtectionPercent": 90.0,
"ProtectionPercentMinimum": 0.0,
"ProtectionSlotsWithoutPenalty": 30.0,
"ProtectionPenaltyPercentPerSlot": 2.0
     18 slots = 100% - this should be 90%
     24 slots = 88% - this should be 90%
     30 slots = 76% - this should be 90%
     42 slots = 52% - this should be 76%

You're right, I was ignoring the protection percent configuration value in the formula.  Please check the new version.

By the way the reason the markers stay up even after you reload the plugin is as far as I'm aware the data for the plugin is not removed when you reload the plugin.  Therefore you need to handle it with the admin command or delete the data file for the plugin.  

A headquarter is not necesarily linked to a TC in a way that if you destroy the TC it destroys the headquarter.. its more like laying claim to the land in that area. In order to claim the land we need to ensure no one else owns that land and a TC sort of already does that so thats why you need to be near your TC to start a HQ.  Typically the TCs are immune to damage with the mod to keep things simpler, however there may be some cases where they end up being destroyed.. like if you blow up the floor or something and the game just destroys it completely so it doesnt float in the air.  In those cases the Headquarter owner should still be capable of redeploying a new TC at the same location of the old one and rebuild the base.