I've uploaded a testmission to repoduce this easily:

1. Start the mission on a dedicated server and connect a headless client to it.
2. Connect as a player to this server, select any of the three slots, don't edit the parameters yet, start the mission.
3. Enter the nearby empty tank as gunner and start killing some enemy vehicles on the runway.
4. In systemchat you will now notice two messages for each kill: "|-> entityKilled EH triggered" Shows up every time any entity gets killed "|---> Handlescore EH triggered" Shows up every time the eventhandler in question triggered on the kill
5. So far this worked fine. Now restart the server, same setup, but this time change the parameter "Headless Client" to "ENABLED" before. Then start the mission.
6. Repeat steps 3 & 4. Now you'll notice that you'll get only "entityKilled" in chat, but "handleScore" should be gone for >90% of the kills.

This shows that the handleScore EH just stopped working.

7. -> Also definitly try exiting the tank and killing vehicles with your launcher and some of the drivers with your rifle through the windows - sometimes the EH will trigger, sometimes not. Inside the tank it mostly will not, with your rifle it somehow will do.

Alternative without my testmission:

1. Create a mission with a player in a tank and several enemy vehicles. Those vehicles MUST be spawned by a headless client.
2. Set up two eventhandlers: "entityKilled" and "handleScore" for the player. Both should trigger some kind of debug messages
3. Start the mission on a dedicated server with a connected headless client.
4. Every time you kill a unit that is spawned by the headless client, the "entityKilled" EH will fire, but the "handleScore" will NOT.
5. Repeat this without the HC. Now "handleScore" will work again.

Although this feels just like a minor issue regarding general gameplay, for missionmakers and scripters this is in fact a huge issue.
This completely prevents custom scoring systems on dedicated servers with headless clients and forces users of such a system to fall back to a server with all units rendered on the server itself, thus creating a performance bottleneck.
Also there is no workaround for this - as long as this EH is broken, custom scoring solutions will not work