Well, now CZ mechanics are different! You win a CZ and suddently enemy ships disappear. So... a part from various bugs, the fact that some CZ are empty, especially after you won.... could be a realistic, a deliberate thing! So it must take some time to have ships again in CZ!!! What do you think about?
I think you might be stating the obvious.
When you win a CZ ships do not magically disappear or should I be saying 'IN my experience ships do not magically disappear'
The remaining enemy ships in my experience either remain, we kill them and they do not respawn, OR.... Enemy ships simply jump into hyperspace leaving behind multiple high wake scans that if we want to, we can scan, butno, they do not magically disappear.
In my experience if I remain in the conflict zone after having won the war, enemy ships MIGHT reappear BUT.... NO GREEN SLIDER BAR, so why fight the things. I confess that I have then jumped out having won that war and YES, it might take 20 or so minutes for the CZ to reset