Are there any versions of Cluedo that do not have exactly 6 suspects, 6 murder weapons, and 9 rooms?
While all printed (the original patent had 10 characters) editions of the classic Cluedo have the standard 6-6-9 ratio, there have been a number of variants that include additional or changed options.
The first variant to include additional characters was the Clue VCR Mystery Game in 1985 with 4 additional options, then followed by Super Cluedo Challenge in 1986 with a 3 additional options of it's own.
The following is a potentially incomplete list of variants with non-standard ratios
(w = weapons, r = rooms, s = suspects, m = murdered):
Yes. One example (and there may well be others) is Super Cluedo, also known as Clue Master Detective. Here is an excerpt of the publisher's description (according to that BGG link, anyway; I can't find the original source):
The late Mr. Boddy's country manor has a total of twelve possible Murder Locations, both outdoors and indoors, with secret passages, plus new "Snoop Spaces" that let you broaden your investigation. A vial of Poison and a Horseshoe bring the number of Weapons up to eight. And the devious bunch of Supsects has grown to ten with the addition of Miss Peach, Monsieur Brunette, Madame Rose and Sergeant Gray.
So it looks like it's 10,8,12, rather than the original's 6,6,9.
Ludology just did a segment on this: http://ludology.libsyn.com/biography-of-a-board-game-2005-cluedo
There are a lot of different versions out there and not all have the 6-6-9 ratio.