Did you ever figure this one out? I'm in a similar boat.

I cannot report success yet since I am just setting this up. But here is my theory, you can go and have a look and try it out:
The CPC Mod has a SpawnGroups.sbc in its Data folder. In this, look up the SpawnGroup with the drone you are looking for.

From there you copy the ID and put it into the SpawnGroup-Blacklist of the MES mod's Confog-General.xml, it should look something like this:
<NpcSpawnGroupBlacklist>
<string>(NPC-CPC) Hacker Drone</string>
</NpcSpawnGroupBlacklist>

My concern is, whether this Prefab-SubtypeId is the one to be used, or whether it is the SpawnGroup-SubtypeId which would be: (CPC)HACKER_DRONE .