Hive should be able to infest wormhole sectors and station sectors. I suggest WH sectors after the regular roid sectors are infested and station sectors last since the bots won't last against the SF. Grey-space only.

+1 to wh and station storms. This is where they would make sense.

Also, I would have a random period of time where the players computer searches out the exit of ion storms in general (despite my loathing of them) as well as for the worm hole or station locations. That this information is immediately available does not make sense. A bit of floundering would not hurt the experience (except at asteroid sector storms which I despise) and could make for better ambush opportunities.

I would not limit this to the magically delicious Grey space. There is no real reason why the SF would deploy automatically against an enemy it can't or hasn't seen.

I think that's the point to the player's ship tumbling randomly after jumping into a storm sector. Storms are particularly nasty for loaded freighters (especially if there's something in there) Fluffy's suggestion makes sense, but I'd eliminate the random tumbling if doing so as well.