top secret clearances are a whole different gambit from secret clearances. They may do some reference checks (I had none that I was aware of, but I know some people did have their friends and family called. May be a "Flag" system), check your credit, make sure you have no felonies, and check your families background (more so if they are nationals of other "high interest" countries).
You will get your clearance before power school, but not neccessarily before you join the navy.
Having a "Secret" security clearance in this context, is just above meaningless, and it basically boils down to the government trusting you with publicly available information. Don't get too caught up in it. Plenty of other jobs have much higher clearances then nukes do.
Finally, you are NOT a nuke until you get through prototype. As far as lecturing security clearances, thats crap, and not your job. Tell the recruiters to get off their butt and do what they are payed to do. You also have no basis to lecture what its like, so the whole thing is odd and confusing.