The Borg effects are the quirkiest. The pets (on MVAM and G-R) get 'unassmilated' on separation and re-assimilate on union. The engine and console add-ons move from the saucer's engines and arrays to the stardrive engine and arrays.
The other effects work. When the saucer isn't attached to the Romulan/Breen/Aegis shield generator, it makes sense that it loses the glow. That rationalizing doesn't work for the MVAM though.
It would make it aesthetially passable (or at least not look half-baked) if the Borg mods had grow/shrink animations and the lighting effects flickered or faded in/out.
Not exactly wailing and gnashing my teeth about it though. Would rather see other things fixed first.