NROTC has a longer training pipeline than some other commissioning routes (that may be the difference).
schmuckatelli's steps are what I've seen on the reserve side for DIRCOM applicants. (My guess is, it is the same for OCS)
The big difference between the Top Secret and Secret clearances is the scope of the background checks. Most (if not all) officers will have Secret Clearance. Only Intel/Crypto... most likely some others, due to the specific job... would require Top Secret.
schmuckatelli also addressed "need to know". Just because you have the clearance, doesn't mean you have access to all the classified data at that level. You still only get what you NEED. (Clearance vs. Access)
And... to answer the question that started the thread - No, not all officers will receive a TS clearance.
IS2 (USNR)