I would go even farther and say that during the TNG era there were also a couple hundred starships in service, which would make the 39 ships lost at Wolf 359 a far more devastating number than if Starfleet had, say, 10,000+ ships at its disposal.
Why, though? It isn't devastating, as we immediately learn: Shelby dismisses the losses as immaterial, easily replaced within the year.
It's a tragedy, and a slap in the face of Starfleet, but it doesn't exactly devastate. And it's part of the TNG writing continuum where the ability to show four intact starships, tops, is described as a deployment of two dozen ships and then dismissed as a peanut-gallery maneuver... The writers wanted it big, and didn't really need to hold back much.
I doubt that was the reason. They probably just pulled "7,000" out of their ass at random.
Also, there are 7,000 active ships, no doubt meaning that many, many more have been retired and scrapped since the NCC registry scheme was created. The newest of the new being NCC-7100 thus wouldn't really fit the picture of there being 7100 NCC-decorated ships out there saving the universe.
Timo Saloniemi