Crannogman, you've not stated your mod list (except for RSRDC). If your using RSRDC v550 only (for the stock game.....no other mods activated with it) I can answer your questions.
Yes, RSRDC is thought to only add historical routes to the game.....it does a lot more. New ships, and planes are added. Configuration files are changed, so are data files.
To answer your question about the Gato (and most later model subs in RSRDC), the sensor file was changed from stock......having the "Ball" mount hydrophone (the one on the bottom of the hull used with newer subs) to require submerging before it works. That's not what it should do, but that's what it does. I'm guessing Lurker had his head filled with Operation Monsun and just forgot that American subs (outside of the S-Class, or a couple of the older class subs) didn't require the sub to be submerged when using a "Ball" mount sensor.
Here's the comparison of the Stock file on the left, RSRDC on the right:
RSRDC requires you to be 12 meters deep before the hydrophone works, when equipped with the hull "Ball" type of Hydrophone. A work around is to remove the "Sensors_sub_US.sim" (found in the Data/Library folder) file from RSRDC.
Regarding not "hearing" a ship even though it's within eyesight of your sub. RSRDC changes the ship route speeds many times in the span of a day. If you've ever opened up one of RSRDC's .mis files, you would see a multitude of way points added to the shipping routes, when compared stock. He has some dropping down to less than 1 knot, then maybe shooting back up to 7 knots on the next way point. The problem is, when your manning the Hydrophone station yourself, you won't hear the target ship as long as its speed is less than halve its MaxSpeed set in its .dat file. Say a ship has a maximum speed of 16 knots....you'll not hear it with the Hydrophone yourself if it's travel speed is 7 knots. This is a stock game issue, not something brought on by RSRDC. However, RSRDC doesn't help the issue by trying to set many of its travel speeds less than halve the ship's MaxSpeed.