Hi Ritzy,
Yes, you are right it is not a good practice because it will impact from logistic point of view because if you remove operative indicator Acc. Assignment Element then those WBS will be bound to not to collect direct cost and there are lots of error that you may face because of untick of Acct. Assignment Element.
Meanwhile, can you check OPSG settings. Go to Component Tab and do the settings as Create/Change/Delete action of material component.
Try this.
Regards,
Amit