When I disable the visuals on the Assimilated Shield, the effect keeps coming back at times. Normally when turning in a battle, it just fades back into view then vanishes again.
Kind of annoying and confusing because I like the shield but not having a Borg ship; what's the point of disabling (or using) it if it won't disable?
What you're seeing is the Borg set procs, the Autonomous Regeneration Sequencer and Multi-Regenerative Shield Array, which only last several seconds. They proc when you're under fire, regardless of whether or not you have the visuals disabled.
Edit: The Autonomous Regenerative Sequencer proc is when parts of your hull glow/flash green, which is probably what you're referring to.
The Multi-Regenerative Shield Array proc is when the actual shield bubble glows/flashes green.