Not much to update, but still nothing from QNAP apart from a request for a logfile which one of our guys sent to them earlier in the week.
As we have "spread the load" to reduce writes to the most severely affected NAS units, we are now experiencing this issue on all of our QNAP NAS units.
The worst affected unit, the TS-859Pro+ now stalls for over 3 and a half minutes, that's ridiculous.
Some other people mentioned free space, from what we see here, that isn't the issue - it's more likely that deleting the files has freed up space in the problem area (journals, directory structures, file allocation tables, your guess is as good as mine). Like someone else posted, some of the NAS units with this issue have over 1TB free, so we're pretty certain that the amount of free space on the volume is not a contributing factor; it's just the amount of directories and files (and their length) that is the root cause of the problem.
It's now more than 9 months since this problem was initially reported... I don't want to swear so there isn't much else to say right now.