Actually there's one trick I know that might allow you to make npcs disappear, but it will require a lot of work since you'll have to build a custom interior map over an ext one one.

Choose a map with a large clearing. Put some platforms at let's say 15m. This will be your ground. Now add a npc on this ground. Now set the platform where the npc stands to hidden state when objective X is complete. The npc will fall. A second platform will appear at the same coordinates when objective Y is complete to recreate your ground. Of course you should take the player to another area of the map and close doors (ie adding closed doors walls over opened ones) or add forcefields in the meantime.

Technically this trick should work but it requires to create interiors from scratch, and this is a very long and tedious task, but if you're ready to do so, then you may use it.

Well, you can also hide the NPC in a wall or inside an object. There are work arounds. For example, in Perilous Prize, I dropped Daimon Tat through a custom stage I created, by removing the floor and then placing the floor back again. But there is no built in function that allows for it.

Supposedly the reason for this is that:

1. Anytime a NPC is removed from a map, be it in a Foundry mission or a Cryptic one, it counts as a "kill" for experience purposes,
2. this hard-and-fast rule apparently cannot be fixed or tweaked without breaking other stuff in the game, and
3. it's too easy to exploit when making farming/grinding missions. (That is, if you could remove NPCs from a map, there'd be nothing to prevent some unscrupulous author from designing a mission that consists of nothing more than beaming onto a ground map that's maxed out with NPC's, and then interacting with an object that makes all the NPCs go away, thereby "killing" them all and instantly "earning" tons of XPs in addition to being too easy a way to grind for dilithium, and now fleet marks as well).

Aren't you confusing npcs and mobs? I didn't pay attention to the effects of the kill button in god mode to see if gives xp for a contact npc but i'm not sure it does...

The only thing that I can think of is if they allowed us to do it with npc contacts, we'd have the ability to do it with mobs. That is the only possible explanation, other than a lack of caring or understanding.

There are no potential exploits in making a contact disappear. But there are with mobs. So, we can't for either? What explains that?

Well the issue initially is that the NPC's i need to get rid of become the mobs witha costume change so i can't use the same NPC that i use for the mobs. Although i'm not really sure how to drop them to a different point on the map.

You can remove the floor and then put a new floor in its place.

As I said, the problem supposedly isn't just that it can be exploited, it's that any fix might end up breaking any number of other aspects of gameplay. Remember, NPCs are among the most commonly used objects in the game; they interact with pretty much everything else on the map. If the devs were to make such drastic changes to such a fundamental class of objects to allow all of them to be turned off (as opposed to just NPCs in mobs) as well as create some kind of means to distinguish between a combat kill and a more general turning-off (in order to defeat the exploit potential), there's no telling what kind of ripple effect those changes will have on gameplay, not just in Foundry missions but across all of STO, or at least Cryptic has decided it's not worth finding out.

That sounds theoretically possible, though melodramatic...

I think the best solution I've heard was allowing us to teleport npcs to a far-flung corner of the map. They could make it so you can't teleport them until any objective they are tied to is complete, that way they would appear to disappear, but nothing gets broken.