I'm using B54 with snow leopard & have no problems with typing either @ or #. Maybe this is something else that doesn't jive with quicksilver > B54. If you want to try B54 you can grab it from the Blacktree site but bear in mind you lose access to the preferences panel. So make sure you're happy with your setup before swapping over. There's also a link to the latest build of quicksilver, B58, there, so even if you don't want to try B54 you'd be well advised to replace your B57 with that.
You also lose scoping for triggers if you try B54. If you do try it keep hold a zipped copy of B58 so if you do need to access preferences you can just quit QS, unzip B58 & re-open QS from B58. I usually just copy it to the desktop & ignore it when it asks if I want to move it to the applications folder. Once you've finished with it, trash the copy of QS from your desktop to avoid quicksilver getting confused. Oh, and if you're using the BezelHUD interface (which doesn't come bundled with QS) the version that works with B54 causes B58 to crash & vice versa.
I'm guessing you need to use @ & # mainly with the twitter plugin or scripts? A really clunky way around your problem could be to add a shelf item with both @ & #, then set a trigger to open QS with this shelf item showing & build your tweet around it. You may already be doing so. Like I say, a very ugly workaround but it'll get both characters into quicksilver for you. Copy them to your clipboard then "put on shelf".