Sorry, I forgot about that fact.
Maybe you could use a workaround: Put an empty system on your map which links all jump gates/holes you want to use in your missions. Set this system to visit = 128 then all lines coming from and to this system won't be visible on the map.
Via mission script you can teleport force the player to use the right jump gate/hole in this system to the one you want to go.

Cloaking works by just adding a cloaking device to a jump gate/hole and then decloak them via mission script.
There is still the problem that you collide with jump gates even if they are cloaked.
To make them not selectable you would also need to parent them to a NON_TARGETABLE object (then you also can enter them only by using mission scripts... or not at all).

A lot of ugly workarounds, but this is the only thing you can do without Hooking the game.

I've made some progress. I cloaked the jumholes/jumpgates so now they're invisible, I've created new entries in the solararch.ini with solar_radius set to 0.0001 so the icons won't appear on the map, and in the system .ini files I've deleted their ids_name so their names won't appear on the map.

But they still show up in the contact list and it's really annoying (especially the jumpgates, which are listed even if you're half way across the map from them).

Anyone have an idea on how I can solve that?

Worked like a charm! Thanks a million for all your help Skotty!