I'm just curious. When you have a job that requires top secret clearance. Actually I'm not sure what clearance level it would be, but the same level for AECF or EOD. Do they do a credit check? If I had debts in the past, but paid them off. Would they see that? Would this be grounds for disqualification?

All things affect your ability to get a clearance, some more than others. A shaky credit history, and I'me speaking of thousands of dollars, is a definite red light.
If your talking about some late payments which have since been paid off it shouldn't present a problem.

A lot of it has to do with wether you disclose the issues up front during the interview without being prompted to do so.
Assuming you have a good "plan" to work with your budget and keep it clean you can even get away with a little "reasonable" debt.

Reasonable debt typically includes mortgages and car payments.
Excessive credit card debt is what they don't like.

So let's say you had a lot of debt paid it off, what do they think of that...

Let's just put it this way, I've always had very good credit and managable debt, until I had a roommate who took advantage of my kindness and ran up a ton of debt on my behalf, now i've always paid it on time and never been to collections, etc. I've been working 2 jobs to get this debt paid off and I plan to have 20k in debt paid off within the next year...

Just curious about getting a regular secret clearance if this would be a problem, now I don't plan to go into the Navy until I get this paid off?