When transforming to or from siege mode shield visuals disappear. This can be fixed by removing and reslotting the shield but only until you transform again.
The deflector effect does not change position at all, and is placed too far back so the rear part is visible when it should not be.
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Can't really help on the deflector end of things as I haven't tried equipping vanity deflectors on my Siege Destroyers.
Edit: I have also noticed that sometimes it seems I regain the visuals of my vanity shields when coming off of Siege mode, but this happens infrequently.
Edit again: I have also noticed that sometimes I will regain visuals even after changing between modes at some point. I'm not quite sure what the trigger is that causes me to randomly regain vanity shield visuals after losing them.