i want to side with the stormcloaks but i like my house in whiterun. plus i have a bunch of stuff there. will i still be able to access the house if we are at war?

Yeah, even the catapults won't wreck your house. Pretty much all that happens is one of the NPC's houses gets wrecked, and a bit of the fence around the tree gets knocked over. But your house should be fine.

I'm not sure about Lydia though, she may or may not try to kill you, I haven't really figured that out yet... (She may stay loyal to Whiterun and try to kill all Stormcloaks, or she might just follow her master to the grave...)