And was everything hunky-dory afterwards? How did all the other heroes in NYC react? (Outside of the X-books). There in lies the trouble with all the heores in one city. Magneto can commit acts of genocide in NYC in X-Men, but in FF or Avengers its like it never happened.
The other major heroes were tricked in to leaving the city and then Magneto stopped them from returning by putting up a magnetic shield, IIRC.
The "death" and subsequent return of Magneto in Chris Claremont's relaunched Excalibur title fed in to the Avengers Disassembled storyline when the "real" Magneto returned from Genosha to claim his daughter.
That led to the House of M and later Decimation, which made the Skrull invasion feasible. Ultimately, the repercussions of Planet X are still being felt even with the Dark Reign and The Siege.