Do you want it show right away? I assume that showing it right away (as soon as possible) will only cause it to fall off even faster and fewer people bother to look at it and possibly upvote it.

I assume that similar to HN meta stories resulting in upvoting trances, seeing [flagged] leads to ignoring the submission.

Tons of stories get flagged—in fact above a certain point threshold the majority do—and in most cases the effect isn't that strong.

The same reason that you can't see the number of votes for comments. If you see [flagged], you're more likely to flag.

I would guess that most front page articles have some number of flags from concern trolls, and the down-weighting effect is probably not linear, so it just wouldn't be very informative.