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Can't add them (why would you want to?) and you can only remove them by either waiting, or, if you want it to go faster, building a Court of Justice and waiting.

EDIT: Or did you mean in the save game? If so, I have no idea.
 
Or you could just F12 and run the province event for "theives guild breakup". The event ID is in the province improvement file I believe.

And if you wanted to remove them from the game couldn't you just remove the "guild forms" event (if you do back it up of course).
 
If I am not mistaken these 3 buildings can only appear through events. So whatever you want to use them for, it won't be things that you will be able to built.

I am not 100% sure on this though.
 
That was what I thought, but I had to check it which I already had done. Here it is:

thieves_guild =
{
lasting_effects =
{
percentage_score = { gold = 0.75 }
percentage_score = { prestige = 0.98 }
percentage_assasination_success = 1.5
pillage_score = { gold = -5 }
}
mountain = no
hills = no
forest = no
plains = no
march = no
desert = no

}

I would say delete the terrain = no and then you should be able to build them. Oh and add some cost and some other stuff.

This way we can just have one of these and add 2 new buildings. :)

Btw just tested and here we go. All the terrains were listed thus it could never be built in any provinces. Here is the screenshot from my change:

screensave4.jpg