I have a party with Korgan, Viconia and Edwin and I've read around the web that if I reach a reputation of 18, Viconia leaves, the other two guys do the same, and I can't find them in-game again.

What'sthe best way to decrease my rep?

You should get a special ability at some point that will decrease your reputation when you use it. I'm not sure what to do before then.

There think I've heard of a mod that might allow you to donate to the shadow thieves to lower rep, much as you might donate to a temple to raise rep.

The easiest way is to find an isolated no-name NPC somewhere in Athkatla, and kill them. If no other NPC sees the deed, nobody else will turn hostile but you'll still get the rep decrease. Beggars and the like, especially in the Bridge District, are good for this. There are also a few houses scattered around that are inhabited, and you can safely kill their owners for a rep decrease. There's a house next to Mae'Var's Guildhall in the Docks, right over Cromwell's house, that has two generic innocents in it at night. If you have a high rep, killing them both can get you more than 10 points of rep decrease. Note that looting their chest while they're still alive can summon guards as well, which can be fun but doesn't actually help your rep any.

Other than randomly killing people for no good reason, there's not much way to decrease rep other than a couple of evil alternatives to quests like the Tirdir or Trademeet quests, or the hidden finale of the Skinner quest. Once you get into ToB your companions won't leave you regardless of your rep, high or low, so you won't have to worry about it then.

I'm not entirely sure about this, but I think this might also work:
When you recruited Viconia, your reputation dropped by 2 points (for recruting a drow).
If you kick her out of the party, and re-recruit her, it might trigger the 2 rep decrease again.

SPOILER:
When I restored and re-recruited Viconia after she was bitten by Bodhi, I got the 2 rep decrease again. That's why I think the above might work.

Note that if you're trying to pursue a romance with Viconia, kicking her out even temporarily will end it.
Another alternative is the bg2 tweak pack, which allows you to keep evil party members even if your rep goes above 18.

Everytime Viconia leaves, you get your 2 reputation points back, so this won't work.