I'm googling, and I do think those numbers include everything in the Federation, even like shuttecraft, runabouts, freighters, passenger ships, and everything in between. I'm reading even for like deep space nine I all estimates I'm finding are like up to twelve hundred starfleet starships at the most, I do feel that's like the upper limits of interest at all for me.
Shuttles, workbees, and other such utility/auxiliary craft can be discounted (they're ten a penny and can be built with little in the way of resources, space and equipment, if VOY is to be believed). Runabouts are individual ships in their own right (they all have individual registry numbers) so if you were to count the number of them in service the number would be very high. Every Federation member would most likely have their own merchant navy as well as possibly a militia/defense force for homeworld security, which again would push the numbers of Federation ships well into the tens of thousands (there are over 150 member worlds after all). Starfleet is shown to operate its own transport and supply ships, as well as hospital and survey vessels, none of which would be deemed as active combat ships, though I suspect they would have a large number of these four types. So outwith the explorer, cruiser and frigate types of ship there is probably quite a lot of Starfleet/Federation hardware flying around that we've only just scratched the surface of.
