I think this MU isn't bad for Ike, I haven't had a whole lot of trouble with it thus far. While getting hit by PK Fire is a pain in the butt (in general), fair and nair seem to pretty well stuff any options Ness has, so just being wary of when you think they'll throw out the PK Fire or otherwise go for a grab, as recovering against ness can be a bit of a pain if they're on top of covering your options. Make sure to fair the PK Thunder away if they try that against your horizontal recovery, else you'll just eat some free damage and still have to come back.
But yea, as Arrei noted, this matchup is particularly good for us when you get Ness offstage one way or another, as a well timed Eruption beats, iirc, all of Ness's options coming back. A runoff fair to disrupt the PKT2 could also work, but that has it's associated risks, but is also easier to pull off if the Ness isn't careful. Overall just play this MU cautiously, as Ness' moves can be painful but do have a bit of endlag which you can punish with a grab combo, which can really start to hurt ness especially at high % when you start to get edgeguard situations going!
Last note: Mix up your DI if they downthrow you. While Ness has followups no matter what you DI, if they consistently are going for fair chains, DI in, as youll go straight up and they'll fly right past you, possibly allowing for you to get a bair in if they aren't careful. At higher %s though I'd stick with DI'ing away (if they dont go for backthrows immediately) so you don't get bopped by an Upair.