The SR-71 is harder to detect and more maneuverable. Also, SAM technology and tracking methods have improved since the cold war. The thing is whoever wants to stop it needs prior warning, so a small country won't see it coming, unless neighbouring allies warn them.
Maybe the SR-71 is harder to detect, but even if this new aircraft is easier to detect...there is virtually nothing you can do to stop it. Intercepting an aircraft that travels 13,000mph or around 4miles per second is impossible...
Not to mention that the SR-71 is highly outdated where there are far superior aircraft like the FA-22 Raptor and something new thats coming out soon, I forget its name right now.