I would go for MACO Shields or Adapted Shield if you have the ressources for it.
One of my characters is using Fleet Elite Covariant Shields and is performing very good tbh. But I'd say the reputation ones are a tick better due the set bonuses and procs.
The only time I run my Elite Fleet shields is when I'm using two Reman set pieces to accelerate plasma torpedoes. The Romulan and Reman set covariant shields have very poor recharge rates, and their 3-item set bonus is pretty close to worthless, so upgrading to Elite Fleet shields was a no-brainer. This set-up also gives my ship +74.7 base defense at 27 impulse with no elusive trait present.
Yeah Nukes get rid of shield resist stacks. Their job is to remove all buffs, not just boff abilities. The resists can build up again quickly if you manage to keep your shields balanced though.
That's strange, because subnucleonic beam's "flavor text" specifically knocks BOFFS off their seats by shaking the target ship's bridge. I guess someone was rehearsing too many camera tilts with dive-rolls at Cryptic