I don't really buy into the Khittomer accords reduction of Connie's either mainly because while I love Star Trek VI, the plot doesn't really make much sense. Obviously the Klingons figured out how to fix their atmosphere and are doing just fine by the 24th century so the whole reduction of arms thing isn't likely. Besides the Federation are explorers not warriors with warships right?
The most logical conclusion was that the connie was just an old design and eventual testbed for new designs such as the Miranda, Constellation, etc. and by the 24th century production of the class had ceased. Regarding the connie at wolf 359, who knows. Maybe there was one lurking about (other than the Republic) taken out of mothball and yes it did seem like those 40 ships were scrapped together rather hastily from the few ships in the immediate vicinity. I mean why send a Challenger and Freedom class against the borg?? Haha
Also when they finally hit Earth you saw no ships at all!!
I think in Season 3 TNG the writers simply wrote with the idea that either Federation ships were far out in space or just not that many (maybe a few 1000) The real world explanation for that was simply not having many studio models. The models that were made for Wolf 359 had been created by the model makers for a script that explicitly called for "smaller ships than the Galaxy." However, by DS9 and First Contact cgi made bigger fleets possible and thus the Federation fleet sized and strength got retconned.