Hulk has a trait that says he can use perplex outwit and shape change, this power can't be ignored does this mean if he is pulse waved does he get shape change, and does he get to roll vs battle fury?

If an effect were to ignore Outwit, Perplex, or Shape Change, that effect fails to do so with this trait. But ONLY ignore... If an effect instead says those powers can't be used, that's different and that effect would indeed prevent their use.

Yes, pulse wave says ignore. Since your ability says can't be ignored, you would be able to roll shape change and your perplex/outwit would remain in effect as well if you used them of course.

I understand why Hulk could use Shape Change against Pulse Wave since the entire ability can't be ignored. But you are saying that also means the standard powers grant can't be ignored individually either? i.e. Battle Fury or some special power that specifically ignored Perplexes?

None of the things granted by WITH EACH NEW DAWN can be ignored. So Battle Fury can't ignore his Shape Change and your hypothetical Perplex ignoring power can't ignore his Perplex.