After fighting Jon Irenicus in Spellhold, I decided not to go with the untrustworthy Saemon and instead went directly to The Underdark through the portal. By doing so, I missed out on Sahuagin City with all it's items and quests... So, if I use CLUAconsole to teleport there (I am currently in chapter 6, gathering allies to fight Bodhi) could this affect my game in any way (cause it to crash etc.), or is it safe to go there? And what is the area code?

In theory that's impossible or it ruins your game, because when you choose to go with Saemon in Spellhold, you are on his ship, and after a while you get a battle with Githyanki (did I spell this right?), after you took care of them, the ship goes down to davy jones locker, Saemon leaves, so if you meet him in Tob you have a problem.
So i don't know if its wise to teleport directly to the city. But if you have a savegame, just load, because the city is a beatiful place with some interesting things, who continue in Tob, and there some components of powerfull weapons to found there, so just load man.