Maybe keeping the shields as is but reducing their submerged movement speed.
Biggest problem I've seen with them is that amphibious units are too slow in water to effectively catch up to the shield balls while hover and ship units have to deal with forced distance padding that water level gives them so they can't get under the shields effectively.
Sea units that should in theory beat sea shield spam is fast units like raiders(Dagger-Seawolf-Hunter) that run in and burn them down while assault units move in and fight the rest of the now unprotected shield-ball. Problem here starts that pretty much most naval shield balls is Shield + Siren + Envoy/Lance.
Sirens have strong AoE to do Riot job and lots of HP letting it tank waves of weaker units charging in while shields and artillery falls back.