No! It does not at all follow from NSA/USG's policy interests that NSA doesn't have secret factoring improvements. As the last few years of crypto research have shown, there's a big difference between having a break and being able to operationalize the break. It's plausible that NSA could have something that is tractable against an individual target, but not against massed targets. In fact: if they have a secret factoring improvement, this is the most likely shape of the problem for them.