I believe these were added to gameplay to give a certain sense of progress to the "beginner-like" players... and provide a simulated random factor.
Indirectly, they really are nothing short of extreme variables which can create some advantages. Specially, the worm-hole incident!
The scattered anomalies also help in establishing contact between races. I don't bother manually exploring to establish trading or diplomacy contacts, because I know that eventually one of their survey ships will encounter one of my ships, or vice-versa. Contact between races wouldn't happen as soon as it does without anomalies. I think that's the main reason there isn't an "off" button: it keeps the races from too much isolated turtling.
P.S. I agree that respawns should follow the original setting for frequency, and that the AI should do a better job of grabbing respawned anomalies.