I think there is plenty of reason to think that these ships are present at the moment. For one thing, Stone looking at the chart to determine where he can grab extra repair crew from suggests that those repair crews are local, not spread throughout the Federation.
Also the fact that this chart is labeled as "% COMPLETE" would seem to suggest that there is work currently happening on these vessels. Ships "still in need to receive essential upgrades" wouldn't have a progress bar like this. One would imagine ships in need would appear as a simple list, with no progress, seeing as how they are not yet being worked on. Doesn't make sense to send out a starship with only 12% of her refit competed, does it?
Besides, what business is it of Commodore Stone's what every ship's refit and repair needs are? It seems more likely to me that he is looking at a chart for just those ship's he is responsible for. I think it's interesting that Stone wears a red shirt. I like to assume that Mendez was still the actual C.O. of the base, but was gone for whatever reason and his "first officer" Stone was in charge while he was away. This might be supported by his title in the closing credits: Portmaster. Why would the portmaster need to know about everyone else's status? He really should just be focused on his own job, I think.
No, while I usually am a little annoyed whenever someone pedantically invokes Occam's Razor, in this case, I really do think that the chart representing those ships actually at the starbase being worked on makes the most reasonable sense. It's the simplest answer, given the context as I see it.