Hypersonic speed ignores hindering terrain? I mean, it doesn't right? Nightcrawler and Flash have to stop once they enter hindering...right?

You are correct. They have to stop when entering hindering terrain.

And are penalized as normal (1/2 move) for starting their action in hindering.

In fact, this is one of my favorite uses of Smoke Cloud in the late (DC) game - use Robin or a damaged Nightwing to throw up hindering terrain and limit Flash's movement options.

Another favorite trick of mine when facing Hypersonic figs is to place an object (hindering terrain, natch) on a stair space of elevated terrain I plan to use. This effectively limits Flash/Nightcrawler's ability to come get you.

Kid Zemo