What Marlin is saying is that none of us can actually give you a 100% accurate answer.
Multiple factors will go into whether those waivers will impact your ability to get into the program, chief of which is the "needs of the Navy", i.e. how many Nukes do they need, how many applying don't need waivers (waiver means more work involved in the process and more time before shipping to boot camp), etc.
We can toss out some educated guesses, but that's all they'll be, guesses.
Best of luck and talk to another recruiter about that signing up for another rate thing. Maybe she's trying to jump-start the security clearance process, but quoting the time-tested statement, "trust but verify".
Best of luck to you!