The main disadvantage of switching the client deletion threshold to one day is that you can't really move clients around effectively.
If you move a client to another group and the record gets deleted over the weekend, it'll check-in and drop back into the "Preferred Group" in the sylink file on Monday (and revert back to whatever policies are there).
Still, bringing the threshold down remains the cleanest way of removing stale/orphaned records, so you'd probably be best off taking down to 1 day, leaving it for 1 working day, then bringing it back up to a normal threshold.
Why are you getting the duplicates anyway? Is this a VDI environment? Have you checked out the smaller threshold that can be applied to non-persistent VMs?