My preferred mode of playing is 3v3 - 6v6 PVP games, I'm 900~1k rated.

Idk, I wouldn't throw this one out of the window just like that.
Subs struggling with jammers makes 100% sense - jammers are kind of useless most of the game anyways in my experience, this would give them some usability (also only available for UEF).
Mid and Late game you have proper intel infrastructure or can spit out a quick scout/spy plane to check things out.
They can also be used to thwart damage from 'passive combat' (units being held back but still being in firing range, say in Setons navy game), or slightly increase survivability of a pack of frontline/infiltration units (though this is probably mostly used by lower rated players - like me).

In naval-enabled maps on the medium and smaller side, a single sub can shut down your naval initiation with a bit of micro management, and the submarine-less player is forced to try a reclaim suicide run with engies (if using the ACU is not an option), build T1 torp launcher, or try to sneakily build another naval yard and hope he won't be detected. But if you are paying any kind of attention or god forbid even actively trying to prevent your enemy from entering the naval theater, you can stop all of those attempts with a single sub (and you'll probably have reinforcements following behind).

Also, it would kind of force players to diversify their navy build, instead of spamming T2/T3 subs mid or late game, which also forces T2/T3 sub response by the defender if the air game is not in his favor to rely on torp bombers.

So having subs be dependent on other sources of intel early game like frigates or scouts, I think it could work well - mid and late game the player will sort of be forced to diversify his unit composition in order to have the subs be useful.

Definitely have surfaced subs have the current 'full' vision radius, but none when submerged, thus forcing the player to surface it and expose it to danger (will also help newer players learn that subs have guns mounted that do extra DPS when surfaced, which is great to dispatch engies or naval yards faster).