I wonder why there are so few philosophers 0 - 1000 AD?

There were actually quite a lot. For instance, there were the Neoplatonists, around the third century, such as Plotinus, Proclus and Porphyry. Then there were the Fathers of the Christian Church, from the third to the fifth centuries. Some of the latter, it is true, do qualify more as theologians than philosophers: but there were also several genuine philosophers among them, such as Origen, Tertullian or Saint Augustine. After that, though, the state of philosophy in this region (and we're talking about the Mediterranean here, from Greece and Rome, through Asia Minor, down to Egypt) did begin to decline. Boethius (d. 524 or 525) is sometimes cited as the last significant philosopher of the classical period, before the Dark Ages properly set in. And I do know what you mean, because then there was quite a striking gap in philosophical activity. The gap might not have been a thousand years, but it probably was two or three hundred. Still, though, things did eventually start to get back on track; and...

In reading various relatively contemporary secondary literature on several different philosophers, I've noticed that many of them seem to intimate (or sometimes outright state) that the philosopher in question has been badly misunderstood, at least from a time shortly after their death, until relatively recently. Has the standards of scholarship really drastically improved in the last 20 or so years, or is this sort of claim perennial to the secondary literature on philosophy?

I think the standards of scholarship have improved over the last twenty years (or maybe the last forty or so -- it's been a gradual development). At least in the better work that is being done in the history of philosophy nowadays, there is a far higher level of rigour than one used to find. This has probably been a consequence of the expansion in the professional field during that period. With so many more academics working on these things than there used to be, all in (friendly) competition with one another, the somewhat woolly and slapdash approach that one can find in older works on the history of philosophy will nowadays lose out in the battle for publication. And the field has definitely benefitted as a result of this new rigour. But that's not necessarily to say that we understand historical philosophers better than they used to be understood. In the academic profession, there's a lot of pressure to come up with some new insight or original interpretation, to validate the publication of...