When you are wanted anywhere in the galaxy (and occasionally, even if you aren't!), Navy interdictions become fairly common (seems to me the longer you are in SC, the more likely it is to happen, but that could be my flawed perception, aside from the obvious logic of it, lol), yes, this was the case before 3.0 and has not changed in 3.0.
Don't shoot before scan.
Seems to be fixed... got a navy interdiction myself a few days ago and was surprised that they actually scanned me.
Tangent: I've had Federal Agent ships come up Wanted after a KWS. Seemed odd. Maybe they're wanted for interdicting innocent (?) CMDRs just trying to go about their business...