Agreed, I have DOpus 5.82 on ths A4000T, the largest disk is an 80Gb drive with the largest partition being 40Gb.
As expected, the "disk free" values shown by DOpus are wrong, so just ignore them. The whole system is completely reliable, no problems with DOpus.
I'd suggest using a decent disk filing system such as PFS3. Also check the MaxTransfer and mask are set correctly in HDtoolbox.
From PFS3's manual:
The MaxTransfer must be divisible by the sector size (usually 512) due to a bug in the Workbench format code. This is done by ending the value with 'e00'.
For example: instead of 0xffffff, use 0xfffe00.
Not sure if this still stands with OS3.9, but something to keep in mind.