You don't need to loadresident or loadmodule icon.library or workbench.library under 3.9. If you need to boot an old game that tries to start workbench to launch it, you could be boned, but you could always softkick for those scenarios.
None of this matters for whdload however.
In answer to the original question, no I don't think you can fit 3.9 in 512kb unless you find special resourced versions of everything that trims every last byte possible, but then I don't think you could fit workbench 45.132 in there too. Easier to just leave out workbench.