It is possible to side-step that by basically proving by preponderance of evidence (i.e. more likely than not) that the failure wasn't knowing and willful. So claiming ignorance especially if the time period to register was pretty thin could work. The thing is that it's up to the agency in question whether to grant it, so that'd be up to the employer or overseeing agency and not the SSS.



Anyways for OP that being said, eligibility for an actual security clearance isn't exactly cut and dry and the higher the clearance you need, the harder they will pull you through the wringer.
Having undocumented parents for example is likely a huge no-go because of the associated risk of blackmail over there.
Similarly foreign citizenships and foreign contacts in general are also a huge mess, best case for you is being from a country that automatically strips it away if you naturalize elsewhere, then it's renunciation, then if you're from a country that makes it neigh impossible to get rid of it is to basically walk away from it. They definitely won't give you one if you actively maintain a foreign passport and go visit grandma every summer.