Hi propbeanie.
No, I haven't got the SJ Upgrade for the S-class boat, all I got for that class was the 20mm Oerlikon single barrel and the improved SD Radar upgrade. Also I got the changed turret for the S-class boat to fit the 20mm Oerlikon.
I have saved before entering the base, I will reload the save and dismiss the new boat and check if I get the SJ-Radar for the pig-boat.
Edit: I reloaded the save and there also was no SJ Radar available for the s-class boat, I was offered an upgrade to the 4in/50cal deck gun tho.