The pool of Americans that can qualify for a clearance is very small. You'd be surprised how many people have poor credit, bad debt, foreclosures, foreign connections, drug use and/or arrest history. It's not a fair comparison to the applicant pool available to your typical industry business. When I got my TS out of college, the OPM agent went to my old frat house and interviewed people at random, then went to my girlfriend's sorority house and interviewed random people there. It can be brutal.
If you are a citizen but your spouse is not a US citizen, does that count as an out? I hard a while ago that having a spouse from China could ruin your chances of getting security clearance, but I’m not sure if naturalizing solves that problem or not.
Yes, it will make a huge impact during the investigation and adjudication process. For TS and TS/SCI, even with naturalization the chances for approval will be slim and naturalization likely won't help, especially if they have family in China. For the government, it's all about calculating risk of someones loyalty, character and having things that can be exploited by financial issues (debt is the biggest disqualifier), foreign contacts or family, and anything they'd want to keep secret that could be used for blackmail.
If they have a good candidate and the only problem is debt, they should offer to pay it off. They have no qualms printing billions to save some broken banks.
None of those disqualify you, necessarily. They are first and foremost concerned about 2 things: can you be honest with them, and can you keep secrets.
Even if both of those were false in the past, you could still pass.
