So I have this german p38 9mm that my dad smuggled home after WW2 that is in great shape. It was made toward the end of the war. It had just sat in the gun case since 1945 with an occasional cleaning.

I fired it and the sights are way off. Shoots like 2 ft low and to the left at 15 yds.

Would it affect the value if I had a gunsmith (or me if I am brave) try to adjust the fixed sights on this gun to make it somewhat accurate?

me too. my grandpa did the same thing as your father however my grandma made him sell it as soon as they had my aunt.

As a Bring Back Piece it has sentimental value, And depending on the MFG Codes/Year may have some monetary value as well....Towards the end of the war production qualitysuffered greatly over the need to turn them out.....That could explain the sights being off....And no reason not to shoot it if you want to

Aligning​ the sights are no big deal for a good 'Smith and shouldn't cost much:

Both the front and rear sights are removable and replaceable....1st I'd buy myself another set of original sights to install and put my originals that came with the pistolaway in case I wanted to put the gun back into it's 100% original state (Did I use the word original enough times??? LOL)

To adjust the elevation the front sight will need milled/filed down to bring up the bore line to target, Take note of the original angle of the sight and preserve it.

To adjust the windage to the right thenpush the rear sight likewise to the right - You may not be able to make up 2 feet of windage before coming all the way to the right of the slide, But it should get you close enough to live with....May also be able to adjust the front one in it's Dove Taila little left and mill away any of the Sight'sDove tail that hangs over the left of the groove.(I can't remember if these are pinned???)

Unless your 110% comfortable doing this yourself take it to a 'Smith - Nothing Screams "Bubba at Work" louder then a beat up set of sights from punches or drifts and a few beat marks on the slide, Also the Dove Tails can be a bit cranky and hard to fit.