The facts
Nuke boats are noisy, reactor driving generator to produce power, a/c, air cleaners, etc. However submerged range is virtually unlimited so the boats were designed for a high underwater cruise speed, long patrol duration but not great at sneaking around.
Diesel / Electric boats are very quiet when they want to be. Battery driving Electiic motor at low speed and few propellor RPMS make them hard to detect. The disadvantages have been limited battery life forces you to run surfaced or near the surface with a Snorkel so that air breathing engines can be run for a) increaed speed and b) charging of the batteries. A side problem in WWII technology is that sea water + lead acid battery = chlorine gas. Boat is excellent going undetected when submerged but has a limited patrolling time Gato had about a 60 day limit and limited submerged duration Gato was about 48 hours max at minimum battery load and obnoxious conditions, no A/C, fresh air, etc. Plus boat desing included motor intake and exhaust requirements which limited depth on dives.
AS best guess
With new battery technology and a a non oxygen buring CO2 engine for recharging a Stirling-Electric boat would make a much better hunter killer than a Nuke. While retaining the deep diving and higherspeeds of a nuke boat.