Were officers on submarines the same as the rest of the Navy?

Yes and no. An ensign was an ensign, and a lieutenant was a lieutenant. However, some were regular officers and some were reserves.

Regular officers enter the Navy through the Naval Academy or through the scholarship program of the Naval Reserve Officers Training Corps. (In spite of the name, the NROTC program graduated both regular and reserve officers.) Regular officers have a minimum service obligation but no definite end date. They serve at the pleasure of the president and request to resign.

Reserve officers enter the Navy through the non-scholarship part of the NROTC program or through various other reserve programs. They may also have come through the Officer Candidate School (OCS). Reserve officers have a contract of a determined length but can be released early. They may also apply to become regular officers.

A significant change during the war was the increase in the number of reserve officers. There were few of them in the Navy when hostilities broke out. At first, reserve officers were looked upon with some skepticism. However, they proved themselves to be capable officers and the submarine war would have been much less effective without them. 

It appears that nearly all submarine commanders were regular officers with most being Naval Academy graduates. It was late 1944 before the first reserve officer would command a submarine in WW2.