It’s not entirely clear what you are measuring… does 1000/s mean files written per second? What’s your benchmarking setup?
In general, a few things are slightly slower with QuarkDB namespace, but in general usage it should not be noticeable. 30% is a significant difference, it would be nice to understand where exactly it’s coming from.
A large amount of changes occurred between 4.4.23 and 4.6.8, so it’s difficult to tell what is the cause of the performance decrease. It would be best to make one change at a time when benchmarking (ie benchmark -> move to 4.6.8 -> benchmark -> move to QDB namespace -> benchmark), to be able to separate the effects of a new version vs a namespace change.
There’s been a few performance optimizations in recent EOS versions to boost the throughput of the QuarkDB namespace, maybe try upgrading to a more recent version than 4.6.8 and let us know if it helps.