Oh they were available as an option before that. My 97 Expedition has rear discs. My dad's 97 F-150 had drums.
The Expedition is a 5.4 with a 9.75 axle. Dad's truck was a 4.6 with an 8.8. I have seen a few later than 99 with drums. We saw a LOT of this era truck during the many multiple waves of the fuel tank strap recall. And even though it was the only thing we were ever going to do on those trucks, we still had to check the brakes for the MPI.
The pattern I noticed was that a 5.4 pretty much always had a 9.75 and rear discs. In fact I can't specifically remember ever seeing a 9.75 with drums.
A 4.6 truck was more likely to have an 8.8 with drums unless it had a tow package.
I think Ford ditched rear drums for the F-series altogether in 04 when they went to a 6-lug axle.
It also seems like the SCREW trucks always got a 9.75, and they became more common to see on the 04+ body than in the 97-03. I don't think they even offered it as an option until 2000.