No doubt. The original reason for a new workbench.library was to fix a few bugs.
No, not exactly. The original reason for updating workbench.library was to produce something which would make AmigaOS 3.5 a more attractive product. As Workbench is the "face" of AmigaOS, changes to make it more responsive (e.g. real-time scrolling) and more attractive (e.g. colourful icons) were at the top of the list. As for bugs, there were not that many to take care of. The code, architectural burdens aside, was in remarkably good shape.
The other half of the necessary changes happened to the workbench.library API, which was opened up, and also supplemented by an ARexx interface.
A simple cleanup and peephole optimizations that saves 10k is just a bonus and not an attempt to fix the AmigaOS 3.9 bloat :/.
Bloat? Well, the most work that went into Workbench itself was intended to open up the APIs, integrate the new icon.library functionality, make Workbench more responsive and of course replace the built-in "Information..." requester.
I wrote the new "Information..." requester from scratch, and it's this part which made workbench.library much larger than it previously used to be.
For the 3.5/3.9 updates we switched from Lattice 'C' 5.04 to SAS/C 6.55, which should have produced better code. But as the optimizer was set for speed (rather than size, stun or kill) the overall size of workbench.library went up rather than down.
Have you tried PeterK's icon.library? It gives a remarkable speedup (including low end systems) without changing the interface. There is a lot possible with assembler but it is a lot of work. It shouldn't be necessary if compilers were doing a better job.
No, I can't say I did. If I never have to see workbench.library or icon.library from the inside I won't regret it

I did my part in updating both (I rewrote icon.library from scratch for the 3.5 update), but like so many programmers before me, I was unable to address the architectural limitations of either. There is only so much you can do if the Workbench design is actively playing against you...