Can a ship get multiple complications(for example one from the core book and one from the into the storm) that make sence (with paying the sp aditional price for into the storm complication)? For example ancient and wise and planet bound for millenia?

No, not by the rules. However, if your GM says you can then so be it. I tend to disallow Planetbound in my game - it's just a bit to munchkin for my tastes.

Into the Storm's histories are not "complications" per se, they're ship packages purchased with SP. And yes, according to Into the Storm they are incompatible.

Also, Happydaze finds something munchkiny? I am stunned.