o.k., as I happen to have the same devices at hand I tried to duplicate your setup:
In DEV_CONFIG (Rev. E.01.00) I simply set up
A: HP-IB 0 0 ( HD on 9133H)
B: HP-IB 0 1 (floppy on 9133H)
C: HP-IB 4 0 (first floppy on 9121D)
D: HP-IB 4 1 (second floppy on 9121D)
I set the 9121D to HP-IB address 4 just because I could - no special reason.
As expected, I can access floppies in all three drives B: C: D: without problems.
Of course, these floppies must be formatted as single sided for the 9121.
So in principle your setup should work too.
BTW: when I prepared my hard disc for MS-DOS 3.20, I also had to set "max. of sector size" in DEV_CONFIG to 1024, otherwise my hard disk would not work (1024 was also set by a jumper on the mainboard of the 9133).
Things to check: