Here are the facts, I am not telling you what you should do one way or the other. For full disclosure, I disclosed my drug usage because I had an arrest on record (expunged, which caused a ton of issues but thats a different story) and didn’t know what clearance investigators had access to.
Polygraphs have been proven, thoroughly, to be incredibly unreliable and essentially pseudoscience. However, the federal government keeps using them as a tool to weed out easily nervous people who are not aware of that fact.
There are two types of polygraphs, and whether you get one or the other or both depends on the federal agency you’re applying to and the position. There is a CI, or counter-intelligence, polygraph where you will be asked questions about foreign contacts, travel you’ve done, if you’re a terrorist, etc. which focuses on if you’re essentially a spy or have connections to other countries whether it be financial or personal.
Then there is a lifestyle polygraph which asks questions about drug usage, sexual preferences, etc. which is designed to see if you lied about any questions relating to that/if you are a “good fit” which really means if you are considered a well-balanced individual without quirks, kinks, or blackmailable habits.
The navy will not polygraph you for either, unless you are under some kind of investigation or possibly require specific TS readins or a higher clearance than a basic TS-SCI. That stands true for 99% of Navy personnel. I’m sure there are some billets that might poly you but I’ve never come across anyone who fit that description.
Navy TS investigators will likely be able to see any information you give the federal government. If there are inconsistencies that they find, this will be a problem.
You are in a sticky situation as you’ve already got an interim secret and didn’t disclose information that the federal agency you’re applying to will likely be able to see.
What you do is up to you. It would have been easier to just tell the truth but we’re past that now. You can always tell your recruiter that you wish to disclose information now and see what they do, it may or may not affect your application and current clearance.